Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications

2010 ◽  
Vol 16 ◽  
pp. 189-211 ◽  
Author(s):  
Peter J. Wagner ◽  
Jonathan D. Marcot
Keyword(s):  
Morphological Change ◽  
Fossil Record ◽  
Phylogenetic Inference ◽  
Nuisance Parameters ◽  
Character State ◽  
Prior Probabilities ◽  
Sampling Intensity ◽  
Future Goals ◽  
Speciation Rates ◽  
Over Time

Quantitative phylogenetic inference estimates the probability of observed character distributions given trees and rates. Most available programs for doing this assume (tacitly or explicitly) that the sampled taxa are contemporaneous. However, paleontologists usually sample taxa over a clade's history. Thus, we must estimate the probability of observed character-state distributions over time given trees and rates. When we include information about sampling intensity, then we really are estimating the probability of the observed record given trees and rates. Some additional problems that should be issues for neontologists, but which are much more obvious concerns for paleontologists include: 1) ancestor-descendant relationships; 2) punctuated versus continuous morphological change; and, 3) the effects of extinction and speciation rates on prior probabilities of trees. Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, our tests of phylogeny are really tests of evolutionary histories.

Quantifying morphological change during an evolutionary radiation of Devonian trilobites

Paleobiology ◽  
2012 ◽  
Vol 38 (2) ◽  
pp. 292-307 ◽  
Author(s):  
Francine R. Abe ◽  
Bruce S. Lieberman
Keyword(s):  
Morphological Change ◽  
Fossil Record ◽  
Character State ◽  
Geometric Morphometric ◽  
Biogeographic Patterns ◽  
Ancestral Character State ◽  
Speciation Rates ◽  
Adaptive Radiations ◽  
Geometric Morphometric Analysis ◽  
Heterogeneous Region

The fossil record provides an important source of data on adaptive radiations, and indeed some of the earliest theoretical insights on the nature of these radiations were made by paleontologists. Here we focus on the diverse DevonianMetacryphaeusgroup calmoniid trilobites, known from the Malvinokaffric Realm, which have been considered a classic example of an adaptive radiation preserved in the fossil record. We use a geometric morphometric analysis in conjunction with phylogenetic and biogeographic patterns and data on speciation rates. Using ancestral character state reconstruction during speciation events, we quantify patterns of morphological change in order to assess the role ecological and geographical factors may have played in mediating this radiation. We found no significant differences between the amount of morphological change that occurred during speciation events when ancestors and descendants were in the same area as opposed to when they occupied different areas. Further, the magnitude of morphological divergence did not change through time or with cladogenetic rank. These patterns, in conjunction with the fact that the radiation occurs in a geographically heterogeneous region subjected to repeated episodes of sea-level rise and fall, suggest that at the macroevolutionary scale this radiation may have been motivated more by phenomena that facilitated geographic isolation than by competition.

scholarly journals Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST

2020 ◽  
Vol 70 (1) ◽  
pp. 181-189
Author(s):  
Guy Baele ◽  
Mandev S Gill ◽  
Paul Bastide ◽  
Philippe Lemey ◽  
Marc A Suchard
Keyword(s):  
High Performance ◽  
Markov Models ◽  
Marginal Likelihood ◽  
Likelihood Estimation ◽  
Phylogenetic Inference ◽  
Time Variability ◽  
Substitution Process ◽  
Wide Range ◽  
Markov Modulated ◽  
Over Time

Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.]

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 What affects power to estimate speciation rate shifts?

2018 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Tree Age ◽  
Character State ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

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?’

Spatiotemporal palaeodiversity patterns of modern crocodiles (Crocodyliformes: Eusuchia)

2019 ◽  
Vol 189 (2) ◽  
pp. 635-656 ◽  
Author(s):  
Ane De Celis ◽  
Iván Narváez ◽  
Francisco Ortega
Keyword(s):  
South America ◽  
Least Squares ◽  
Late Miocene ◽  
North American ◽  
Fossil Record ◽  
Generalized Least Squares ◽  
Global Scale ◽  
Biotic Factors ◽  
Species Dynamics ◽  
Over Time

Abstract Eusuchia is a crocodyliform clade with a rich and diverse fossil record dating back to the Mesozoic. There are several recent studies that analyse crocodyliform palaeodiversity over time, but none of them focuses exclusively on eusuchians. Thus, we estimated subsampled eusuchian palaeodiversity species dynamics over time not only at a global scale, but also by continents and main crocodylian lineages (Alligatoroidea, Crocodyloidea and Gavialoidea). These estimates reveal complex spatiotemporal palaeodiversity patterns, in which two maxima can be detected: the first during the Palaeocene and the second, which is also the biggest, in the middle-late Miocene. The Palaeocene shift is related to a North American alligatoroid diversification, whereas the middle–late Miocene maximum is related to a diversification of the three main Crocodylia lineages in Gondwanan land masses, but especially in South America. Additionally, a model-based study using generalized least squares was carried out to analyse the relationships between different abiotic and sampling proxies and eusuchian palaeodiversity. The results show that palaeotemperature is the most important factor amongst the analysed proxies, in accordance with previous studies. However, the results suggest that, along with palaeotemperature, other abiotic and/or biotic factors might also be driving eusuchian palaeodiversity dynamics.

scholarly journals A62 A major likelihood-based approach gives problematic estimates of diversification dynamics and rates

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Chenlu Di ◽  
Andreas L S Meyer ◽  
John J Wiens
Keyword(s):  
R Package ◽  
Change Over Time ◽  
Diversity Patterns ◽  
Significant Relationships ◽  
Correct Model ◽  
Speciation Rates ◽  
Incorrect Model ◽  
Diversity Of Life ◽  
Over Time

Abstract The diversity of life is shaped by rates of speciation and extinction, and so estimating these rates correctly is crucial for understanding diversity patterns among clades, regions, and habitats. In 2011, Morlon and collaborators developed a promising likelihood-based approach to estimate speciation and extinction and to infer the model describing how these rates change over time based on AICc. This approach is now implemented in an R package (RPANDA). Here, we test the accuracy of this approach under simulated conditions, to evaluate its ability to correctly estimate rates of speciation, extinction, and diversification (speciation—extinction) and to choose the correct underlying model of diversification (e.g. constant or changing rates of speciation and extinction over time). We found that this likelihood-based approach frequently picked the incorrect model. For example, with changing speciation rates over time, the correct model was chosen in only ∼10 per cent of replicates. There were significant relationships between true and estimated speciation rates using this approach, but relationships were weak when speciation rates were constant within clades. Relationships were consistently weak between true and estimated rates of extinction and of diversification. Overall, we suggest that results from this approach should be interpreted with considerable caution.

Evolutionary Patterns in the History of Permo-Triassic and Cenozoic Synapsid Predators

2002 ◽  
Vol 8 ◽  
pp. 267-288 ◽  
Author(s):  
Blaire Van Valkenburgh ◽  
Ian Jenkins
Keyword(s):  
Fossil Record ◽  
Late Carboniferous ◽  
Second Phase ◽  
Evolutionary Patterns ◽  
Large Size ◽  
Jaw Mechanics ◽  
History Of ◽  
Trends Over Time ◽  
Energetic Constraints ◽  
Over Time

Synapsids include modern mammals and their fossil ancestors, the non-mammalian synapsids, or ‘mammal-like reptiles' of old classifications. The synapsid fossil record extends from the Late Carboniferous to the present, a span of nearly 300 million years. However, it can be broken into two distinct phases of diversification, separated by about 150 million years. The first phase extends from the Late Carboniferous to the mid-Triassic, includes the first large land predators on Earth, and is almost entirely non-mammalian. The second phase begins about 65 million years ago after the demise of the dinosaurs, includes only mammals, and extends to the present. In this overview of synapsid predators, we emphasize terrestrial species of large size, and their adaptations for killing and feeding, rather than locomotion. Despite fundamental differences in jaw mechanics and tooth morphology, there are significant parallels in the non-mammalian and mammalian radiations of synapsid predators. Both groups evolve sabertooth forms more than once, and both evolve short-snouted, powerful biting forms. In addition, both the Late Carboniferous—Triassic and Cenozoic phases are characterized by repeated patterns of clade replacement, in which one or a few clades evolve large size and seem to dominate the carnivore guild for several million years, but then decline and are replaced by new taxa. Moreover, within both ancient and Cenozoic predator clades, there are parallel trends over time toward increased body size and hypercarnivory that likely result from a combination of interspecific competition and energetic constraints.

scholarly journals Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

2019 ◽  
Vol 68 (5) ◽  
pp. 698-716 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Ancestral Character State ◽  
State Models ◽  
Hidden States ◽  
New Framework

Abstract Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

Long/Short Term Influences on Change

1999 ◽  
Vol 9 ◽  
pp. 309-318
Author(s):  
Kaustuv Roy
Keyword(s):  
Fossil Record ◽  
The Other ◽  
Short Term ◽  
Geologic Time ◽  
Number Of Species ◽  
Higher Taxa ◽  
Terrestrial Habitats ◽  
History Of ◽  
Using Data ◽  
Over Time

Change has been the rule in the history of life. Mammals today dominate the terrestrial habitats where dinosaurs once held sway. In modern oceans, ecologists can study many species of arthropods, but trilobites are long gone. Using data from the fossil record, David Raup estimated that only about one in a thousand species that ever lived on this planet is still alive today (Raup, 1991). On the other hand, the number of species and higher taxa has increased steadily over geologic time. Thus the history of life is essentially a history of turnover of species, lineages and higher taxa over time.

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