scholarly journals The probability distribution of the reconstructed phylogenetic tree with occurrence data

2019 ◽  
Author(s):  
Ankit Gupta ◽  
Marc Manceau ◽  
Timothy Vaughan ◽  
Mustafa Khammash ◽  
Tanja Stadler

AbstractWe consider a homogeneous birth-death process with incomplete sampling. Three successive sampling schemes are considered. First, individuals can be sampled through time and included in the tree. Second, they can be occurrences which are sampled through time and not included in the tree. Third, individuals reaching present day can be sampled and included in the tree. Upon sampling, individuals are removed (i.e. die).The outcome of the process is thus composed of the reconstructed evolutionary tree spanning all individuals sampled and included in the tree, and a timeline of occurrence events which are not placed along the tree. We derive a formula allowing one to compute the joint probability density of these, which can readily be used to perform maximum likelihood or Bayesian estimation of the parameters of the model.In the context of epidemiology, our probability density allows us to estimate transmission rates through a joint analysis of epidemiological case count data and phylogenetic trees reconstructed from pathogen sequences. Within macroevolution, our equations are the basis for taking into account fossil occurrences from paleontological databases together with extant species phylogenies for estimating speciation and extinction rates. Thus, we provide the theoretical framework for bridging not only the gap between phylogenetics and epidemiology, but also the gap between phylogenetics and paleontology.

2021 ◽  
Author(s):  
Andrew J. Helmstetter ◽  
Sylvain Glemin ◽  
Jos Käfer ◽  
Rosana Zenil-Ferguson ◽  
Hervé Sauquet ◽  
...  

AbstractEstimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenies, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineage-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models and inferences to disentangle diversification histories. Using simulations we demonstrate the characteristics of pulled diversification rates and their utility. We recognize the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenies has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.


2021 ◽  
Author(s):  
Andrew J Helmstetter ◽  
Sylvain Glemin ◽  
Jos Käfer ◽  
Rosana Zenil-Ferguson ◽  
Herv Sauquet ◽  
...  

Abstract Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.


1992 ◽  
Vol 6 ◽  
pp. 133-133
Author(s):  
Steven D'Hondt

Planktic foraminiferal species are generally assigned to higher taxa on the basis of shared morphologic characters and stratigraphic age. These assignments are usually justified on the basis of apparent phyletic relationships. Extant species assigned to the same genera usually exhibit similar trophic and reproductive behavior and are associated with similar watermasses. Paleogeographic and stable isotopic data suggest that coeval fossil species also generally exhibit similar paleoecologic and paleoceanographic associations within well-constrained genera.Despite shared morphologic characters and stratigraphic and paleoenvironmental associations, many higher taxa of planktic foraminifera are not believed to be monophyletic. Many superspecific taxa are widely accepted as paraphyletic (i.e. Guembelitria, Heterohelix). Such paraphyly has commonly resulted from maintaining a different generic or familial name for descendant species that diverge strongly from their ancestral bauplan. Additionally, some higher taxa appear to be polyphyletic (i.e. Eoglobigerinidae, Globorotalia).As presently defined, superspecific taxa–commonly paraphyletic–can generally be used to examine relative radiation and extinction rates within and between different planktic foraminiferal adaptive zones. For example, analysis of Paleocene genera demonstrates rapid earliest Paleocene origination and radiation of sea-surface-dwelling and deeper-dwelling biserial and trochospiral genera. This earliest Paleocene radiation is quickly followed by disappearance of these surface-dwelling genera and some deeper-dwelling genera, in turn followed by major radiation within new surface-dwelling trochospiral genera in the mid and Late Paleocene. Such analysis documents the relative diversity and succession of major adaptive groups, regardless of their phylogenetic relationships.The phyletic status of existing superspecific taxa does not preclude macroevolutionary study of monophyletic groups—or require that presently paraphyletic taxa be subsumed into larger monophyletic taxa. It simply requires that study of monophyletic groups be explicitly based on cladograms or phylogenetic trees. Such studies can address topics of clear macroevolutionary interest, including (i) the relative diversity and longevity of different monophyletic groups and (ii) general patterns of origination and extinction within clades. Additionally, while phylogenetic analysis is not necessary to determine patterns of succession and diversity of within and between adaptive groups, it can amplify our understanding of such patterns. For example, the earliest Paleocene appears to be marked by extremely rapid radiation within two monophyletic groups. The first reaches peak diversity within the earliest Paleocene and dominates earliest Paleocene planktic foraminiferal assemblages, but decreases radically in diversity and abundance within the Early Paleocene. The second continues to diversify throughout the Paleocene and dominates mid and Late Paleocene faunas. Consideration of phylogenetic and paleoecologic relationships within and between both monophyletic groups clearly reveals convergent evolution of deep and surface-dwelling morphotypes, and of biserial and trochospiral forms.


2019 ◽  
Author(s):  
Marc Manceau ◽  
Ankit Gupta ◽  
Timothy Vaughan ◽  
Tanja Stadler

AbstractWe consider a homogeneous birth-death process with three different sampling schemes. First, individuals can be sampled through time and included in a reconstructed tree. Second, they can be sampled through time and only recorded as a point ‘occurrence’ along a timeline. Third, extant individuals are sampled and included in the reconstructed tree with a fixed probability. We further consider that sampled individuals can be removed or not from the process, upon sampling, with fixed probability.Given an outcome of the process, composed of the joint observation of a reconstructed phylogenetic tree and a record of occurrences not included in the tree, we derive the conditional probability distribution of the population size any time in the past. We additionally provide an algorithm to simulate ancestral population size trajectories given the observation of a reconstructed tree and occurrences.This distribution can readily be used to perform inferences of the ancestral population size in the field of epidemiology and macroevolution. In epidemiology, these results will pave the way towards jointly considering data from case count studies and reconstructed transmission trees. In macroevolution, it will foster the joint examination of the fossil record and extant taxa to reconstruct past biodiversity.


2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  

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.


Water ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 472
Author(s):  
Jue Lin-Ye ◽  
Manuel García-León ◽  
Vicente Gràcia ◽  
María Ortego ◽  
Piero Lionello ◽  
...  

Storm surges are one of the main drivers for extreme flooding at the coastal areas. Such events can be characterized with the maximum level in an extreme storm surge event (surge peak), as well as the duration of the event. Surge projections come from a barotropic model for the 1950–2100 period, under a severe climate change scenario (RCP 8.5) at the northeastern Spanish coast. The relationship of extreme storm surges to three large-scale climate patterns was assessed: North Atlantic Oscillation ( N A O ), East Atlantic Pattern ( E A W R ), and Scandinavian Pattern ( S C ). The statistical model was built using two different strategies. In Strategy #1, the joint probability density was characterized by a moving-average series of stationary Archimedean copula, whereas in Strategy #2, the joint probability density was characterized by a non-stationary probit copula. The parameters of the marginal distribution and the copula were defined with generalized additive models. The analysis showed that the mean values of surge peak and event duration were constant and were independent of the proposed climate patterns. However, the values of N A O and S C influenced the threshold and the storminess of extreme events. According to Strategy #1, the variance of the surge peak and event duration increased with a fast shift of negative S C and a positive N A O , respectively. Alternatively, Strategy #2 showed that the variance of the surge peak increased with a positive E A W R . Both strategies coincided in that the joint dependence of the maximum surge level and the duration of extreme surges ranged from low to medium degree. Its mean value was stationary, and its variability was linked to the geographical location. Finally, Strategy #2 helped determine that this dependence increased with negative N A O .


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