Principles Of Paleontology
01 Jan 2016-
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Citations
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TL;DR: A new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record is presented and represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
Abstract: The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.(BDMCMC; biodiversity trends; Birth-death process; incomplete fossil sampling; macroevolution; species rise and fall.)
163 citations
Cites background or methods from "Principles Of Paleontology"
...Our model allows for continuous time and avoids the use of predefined, discrete time bins that are dictated by the geological record and do not necessarily correspond to biological processes (Foote and Miller 2007)....
[...]
...The prior probability of s and e given and is calculated, based on (Keiding 1975), as P(s,e| , )∝ B De−( + )S (9) where B and D are the numbers of speciation and extinction events, and S is the total time lived (Foote and Miller 2007), which is summed over all species: S= N∑ i=1 si −ei....
[...]
...where B and D are the numbers of speciation and extinction events, and S is the total time lived (Foote and Miller 2007), which is summed over all species:...
[...]
TL;DR: Five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification are presented.
Abstract: The foundations of several disciplines can be expressed as simple quantitative laws, for example, Newton's laws or the laws of thermodynamics. Here I present five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification. These statements of our palaeobiological knowledge constitute a dimension largely hidden from view when studying the living biota, which are nonetheless crucial to the study of evolution and ecology even for groups with poor or non-existent fossil records. These laws encapsulate: the critical fact of extinction; that species are typically geologically short-lived, and thus that the number of extinct species typically dwarfs the number of living species; that extinction and origination rates typically have similar magnitudes; and, that significant extinction makes it difficult to infer much about a clade's early history or its current diversity dynamics from the living biota alone. Although important strides are being made to integrate these core palaeontological findings into our analysis of the living biota, this knowledge needs to be incorporated more widely if we are to understand their evolutionary dynamics.
153 citations
TL;DR: A flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model is developed, and calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades.
Abstract: Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
99 citations
Cites background or methods from "Principles Of Paleontology"
...This optimization was performed separately for the lower and upper bound of estimate of Foote and Miller (2007)....
[...]
...The resulting estimate of 0.15–0.30 (Foote and Miller 2007) thus represents the probability that one or more members of a given genus are sampled from a geological time interval, and Foote and Sepkoski (1999) used 5 myr time intervals in their analysis....
[...]
...30 (Foote and Miller 2007) thus represents the probability that one or more members of a given genus are sampled from a geological time interval, and Foote and Sepkoski (1999) used 5 myr time intervals in their analysis....
[...]
...The specieslevel sampling rate was optimized until the resulting proportion of sampled genera was sufficiently close to the genus-level estimate of Foote and Miller (2007)....
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TL;DR: Prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils are reviewed, including the inclusion of a deep‐time perspective based on high‐resolution microf fossil records may be an important step for the further maturation of Macroecology.
Abstract: There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross-scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep-time perspective based on high-resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.
85 citations
Additional excerpts
...The word ‘palaeoecology’ has been used in a broad sense (i.e. the study of the interrelationships between ancient organisms and the palaeoenvironments in which they lived: Foote & Miller, 2007), and most commonly applied to palaeoenvironmental reconstruction using fossil species’ autoecology....
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...Foote, M. & Miller, A. I. (2007)....
[...]
TL;DR: Ideally, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera, and greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
Abstract: Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led—perhaps inadvertently—to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera are suitable proxies for species. This is problematic on both ontological and epistemological grounds. Genera are arbitrarily circumscribed, non-equivalent, often paraphyletic, and sometimes polyphyletic collections of species. They are useful tools for communication but have no theoretical or biological reality of their own and, whether monophyletic or not, cannot themselves operate in the evolutionary process. Attributes considered important for understanding macroevolution—e.g., geographic ranges, niche breadths, and taxon durations—are frequently variable among species within genera and will be inflated at the generic level, especially in species-rich genera. Consequently, the meaning(s) of results attained at the generic level may not “trickle down” in any obvious way that elucidates our understanding of evolution at the species level. Ideally, then, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera. Where genera are used, greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
82 citations
Cites background from "Principles Of Paleontology"
...…debated topics in biology (e.g., de Queiroz 2007; Hausdorf 2011; Mayden 2013), and there has been extensive discussion about whether species recognized in the fossil record should be considered equivalent to species recognized in the Recent (e.g., Imbrie 1957; Raup and Stanley 1978; Allmon 2014)....
[...]
References
More filters
TL;DR: A new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record is presented and represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
Abstract: The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.(BDMCMC; biodiversity trends; Birth-death process; incomplete fossil sampling; macroevolution; species rise and fall.)
163 citations
TL;DR: Five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification are presented.
Abstract: The foundations of several disciplines can be expressed as simple quantitative laws, for example, Newton's laws or the laws of thermodynamics. Here I present five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification. These statements of our palaeobiological knowledge constitute a dimension largely hidden from view when studying the living biota, which are nonetheless crucial to the study of evolution and ecology even for groups with poor or non-existent fossil records. These laws encapsulate: the critical fact of extinction; that species are typically geologically short-lived, and thus that the number of extinct species typically dwarfs the number of living species; that extinction and origination rates typically have similar magnitudes; and, that significant extinction makes it difficult to infer much about a clade's early history or its current diversity dynamics from the living biota alone. Although important strides are being made to integrate these core palaeontological findings into our analysis of the living biota, this knowledge needs to be incorporated more widely if we are to understand their evolutionary dynamics.
153 citations
TL;DR: A flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model is developed, and calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades.
Abstract: Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
99 citations
TL;DR: Prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils are reviewed, including the inclusion of a deep‐time perspective based on high‐resolution microf fossil records may be an important step for the further maturation of Macroecology.
Abstract: There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross-scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep-time perspective based on high-resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.
85 citations
TL;DR: Ideally, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera, and greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
Abstract: Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led—perhaps inadvertently—to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera are suitable proxies for species. This is problematic on both ontological and epistemological grounds. Genera are arbitrarily circumscribed, non-equivalent, often paraphyletic, and sometimes polyphyletic collections of species. They are useful tools for communication but have no theoretical or biological reality of their own and, whether monophyletic or not, cannot themselves operate in the evolutionary process. Attributes considered important for understanding macroevolution—e.g., geographic ranges, niche breadths, and taxon durations—are frequently variable among species within genera and will be inflated at the generic level, especially in species-rich genera. Consequently, the meaning(s) of results attained at the generic level may not “trickle down” in any obvious way that elucidates our understanding of evolution at the species level. Ideally, then, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera. Where genera are used, greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.
82 citations