scholarly journals The effects of taxonomic standardization on sampling-standardized estimates of historical diversity

2006 ◽  
Vol 274 (1608) ◽  
pp. 439-444 ◽  
Author(s):  
Peter J Wagner ◽  
Martin Aberhan ◽  
Austin Hendy ◽  
Wolfgang Kiessling
Keyword(s):  
Fossil Record ◽  
Raw Data ◽  
Diversity Patterns ◽  
Genus Level ◽  
Extinction Rates ◽  
Diversity Studies ◽  
Diversity Dynamics ◽  
Over Time

Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species is identified, but after vetting the genus to which the species is assigned. Extensive generic reassignments elevate origination and extinction rates within Palaeozoic gastropods and origination rates within Cenozoic bivalves. However, vetting increases generic richness markedly only for Cenozoic bivalves, and even then the increase is less than 10%. Moreover, the patterns of standing generic richness are highly similar under all three data treatments. Unless our results are unusual, taxonomic standardization can elevate diversity dynamics in some cases, but it will not greatly change inferred richness over time.

How does species richness accumulate over time?

2019 ◽  
pp. 189-212
Author(s):  
Timothy G. Barraclough
Keyword(s):  
Phylogenetic Trees ◽  
Species Turnover ◽  
Neutral Theory ◽  
Diversity Patterns ◽  
Extinction Rates ◽  
Neutral Theory Of Biodiversity ◽  
Per Se ◽  
Long Timescales ◽  
Over Time ◽  
Structure Diversity

Species are units for understanding the evolution of diversity over large geographical scales and long timescales. This chapter investigates the processes causing proliferation and demise of species diversity within lineages and regions. Phylogenetic approaches have focused on documenting speciation and extinction rates, but mechanistic theory explaining variation in rates is scarce. Diversity patterns are better explained by geographical and ecological opportunity than by correlates of speciation and extinction rates per se. The neutral theory of biodiversity provides a framework that can be adapted to predict diversity patterns in terms of limits due to competition for space and resources, and species turnover (which cannot be detected directly from phylogenetic trees). These theories bring macroevolutionary and microevolutionary theories closer together. In particular, diversity patterns are the outcome of individual selection and dispersal playing out over long timescales. Some of the processes influencing species patterns can also structure diversity at higher taxonomic levels.

Numerical experiments with model monophyletic and paraphyletic taxa

Paleobiology ◽  
1993 ◽  
Vol 19 (2) ◽  
pp. 168-184 ◽  
Author(s):  
J. John Sepkoski ◽  
David C. Kendrick
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Mass Extinction ◽  
Fossil Record ◽  
Numerical Experiments ◽  
Mass Extinctions ◽  
Diversity Patterns ◽  
Extinction Rates ◽  
Low Levels

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere “taxonomic noise” in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

DIFFERENCES IN EXTINCTION RATES EXPLAIN CONTRASTING REGIONAL DIVERSITY PATTERNS IN MODERN TROPICAL BRYOZOANS

2017 ◽  
Author(s):  
Jeremy B.C. Jackson ◽  
◽  
Emanuela Di Martino ◽  
Paul D. Taylor ◽  
Kenneth G. Johnson
Keyword(s):  
Diversity Patterns ◽  
Regional Diversity ◽  
Extinction Rates

scholarly journals Historical evolutionary information in the traditional Linnean hierarchy

1992 ◽  
Vol 6 ◽  
pp. 16-16 ◽  
Author(s):  
Richard K. Bambach ◽  
J. John Sepkoski
Keyword(s):  
Fossil Record ◽  
Latitudinal Gradients ◽  
Evolutionary Information ◽  
Simulation Studies ◽  
Biological Organization ◽  
Diversity Patterns ◽  
Higher Taxa ◽  
History Of ◽  
The Stability ◽  
And Function

The first two ranks above the species level in the traditional Linnean hierarchy — the genus and family — are species based: genera have been erected to unify groups of morphologically similar, closely related species and families have been erected to group genera recognized as closely related because of the shared morphologic characteristics of their species. Diversity patterns of traditional genera and families thus appear congruent with those of species in (a) the Recent (e. g., latitudinal gradients in many groups), (b) compilations of all marine taxa for the entire Phanerozoic (including the stage level), (c) comparisons through time within individual taxa (e. g., Foraminifera, Rugosa, Conodonta), and (d) simulation studies. Genera and families often have a more robust fossil record of diversity than species, especially for poorly sampled groups (e. g., echinoids), because of the range-through record of these polytypic taxa. Simulation studies indicate that paraphyly among traditionally defined taxa is not a fatal problem for diversity studies; in fact, when degradation of the quality of the fossil record is modelled, both diversity and rates of origination and extinction are better represented by including paraphyletic taxa than by restricting data to monophyletic clades. This result underscores the utility of traditional rank-based analyses of the history of diversity.In contrast, the three higher ranks of the Linnean hierarchy — orders, classes and phyla — are defined and recognized by key character complexes assumed to be rooted deep in the developmental program and, therefore, considered to be of special significance. These taxa are unified on the basis of body plan and function, not species morphology. Even if paraphyletic, recognition of such taxa is useful because they represent different functional complexes that reflect biological organization and major evolutionary innovations, often with different ecological capacities. Phanerozoic diversity patterns of orders, classes and phyla are not congruent with those of lower taxa; the higher groups each increased rapidly in the early Paleozoic, during the explosive diversification of body plans in the Cambrian, and then remained stable or declined slightly after the Ordovician. The diversity history of orders superficially resembles that of lower taxa, but this is a result only of ordinal turnover among the Echinodermata coupled with ordinal radiation in the Chordata; it is not a highly damped signal derived from the diversity of species, genera, or families. Despite the stability of numbers among post-Ordovician Linnean higher taxa, the diversity of lower taxa within many of these Bauplan groups fluctuated widely, and these diversity patterns signal embedded ecologic information, such as differences in flexibility in filling or utilizing ecospace.Phylogenetic analysis is vital for understanding the origins and genealogical structure of higher taxa. Only in such fashion can convergence and its implications for ecological constraints and/or opportunities be understood. But blind insistence on the use of monophyletic classifications in all studies would obscure some of the important information contained in traditional taxonomic groupings. The developmental modifications that characterize Linnean higher taxa (and traditionally separate them from their paraphyletic ancestral taxa) provide keys to understanding the role of shifting ecology in macroevolutionary success.

scholarly journals The fossil record of whip spiders: the past of Amblypygi

PalZ ◽  
2021 ◽  
Author(s):  
Carolin Haug ◽  
Joachim T. Haug
Keyword(s):  
Fossil Record ◽  
3D Imaging ◽  
Three Dimensional ◽  
Dorsal Shield ◽  
Stereo Images ◽  
Geological Time ◽  
High Quality ◽  
The Past ◽  
Over Time

AbstractWhip spiders (Amblypygi), as their name suggests, resemble spiders (Araneae) in some aspects, but differ from them by their heart-shaped (prosomal) dorsal shield, their prominent grasping pedipalps, and their subsequent elongate pair of feeler appendages. The oldest possible occurrences of whip spiders, represented by cuticle fragments, date back to the Devonian (c. 385 mya), but (almost) complete fossils are known from the Carboniferous (c. 300 mya) onwards. The fossils include specimens preserved on slabs or in nodules (Carboniferous, Cretaceous) as well as specimens preserved in amber (Cretaceous, Eocene, Miocene). We review here all fossil whip spider specimens, figure most of them as interpretative drawings or with high-quality photographs including 3D imaging (stereo images) to make the three-dimensional relief of the specimens visible. Furthermore, we amend the list by two new specimens (resulting in 37 in total). The fossil specimens as well as modern whip spiders were measured to analyse possible changes in morphology over time. In general, the shield appears to have become relatively broader and the pedipalps and walking appendages have become more elongate over geological time. The morphological details are discussed in an evolutionary framework and in comparison with results from earlier studies.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Complexity and Relative Complexity in Generative Grammar

2021 ◽  
Vol 6 ◽  
Author(s):  
Frederick J. Newmeyer
Keyword(s):  
Generative Grammar ◽  
Simple Theory ◽  
Raw Data ◽  
Complex Theory ◽  
Relative Complexity ◽  
History Of ◽  
Over Time

The notions of “complexity” and its antonym “simplicity” have played an important role in the history of generative grammar. However, these terms have been used in different ways. There have been discussions about whether the raw data is complex (or not), about whether a particular theory is complex (or not), and about whether a particular analysis is complex (or not). This article both sorts out the various uses of these terms in the history of generative grammar and demonstrates that motivations have changed over time for whether a complex theory or a simple theory is more desirable. The article concludes with a discussion of the issue of relative complexity in generative grammar, that is, whether the theory embodies the possibility that a grammar of one language can be more or less complex than the grammar of another.

3. Extinction in the past

2019 ◽  
pp. 33-50
Author(s):  
Paul B. Wignall
Keyword(s):  
Fossil Record ◽  
The Past ◽  
Extinction Rates ◽  
History Of ◽  
Extinction Events

Despite the less-than-perfect nature of the fossil record, it still provides a unique window on the history of life, and reveals that there have been dramatic fluctuations in extinction intensities since complex life evolved around 600 million years ago. ‘Extinction in the past’ considers Jack Sepkoski’s database compiled in the 1980s, and his series of highly informative charts showing both diversity and extinction rates since the start of the Cambrian Period 541 million years ago. The calculation of extinction rates and the improved dating of extinction events are discussed, along with the extinction trends that can be observed. Fossils also provide valuable evidence on the nature of selection during extinction.

scholarly journals How predictable is extinction? Forecasting species survival at million-year timescales

2019 ◽  
Vol 374 (1788) ◽  
pp. 20190392 ◽  
Author(s):  
Peter Smits ◽  
Seth Finnegan
Keyword(s):  
Fossil Record ◽  
Human Impacts ◽  
Rank Order ◽  
Extinction Risk ◽  
Geographical Range ◽  
The Past ◽  
The Future ◽  
Out Of Sample ◽  
Extinction Events ◽  
Over Time

A tenet of conservation palaeobiology is that knowledge of past extinction patterns can help us to better predict future extinctions. Although the future is unobservable, we can test the strength of this proposition by asking how well models conditioned on past observations would have predicted subsequent extinction events at different points in the geological past. To answer this question, we analyse the well-sampled fossil record of Cenozoic planktonic microfossil taxa (Foramanifera, Radiolaria, diatoms and calcareous nanoplankton). We examine how extinction probability varies over time as a function of species age, time of observation, current geographical range, change in geographical range, climate state and change in climate state. Our models have a 70–80% probability of correctly forecasting the rank order of extinction risk for a random out-of-sample species pair, implying that determinants of extinction risk have varied only modestly through time. We find that models which include either historical covariates or account for variation in covariate effects over time yield equivalent forecasts, but a model including both is overfit and yields biased forecasts. An important caveat is that human impacts may substantially disrupt range-risk dynamics so that the future will be less predictable than it has been in the past. This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’

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