Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration

Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume that all samples are tips, they do not allow for this possibility. We have developed and implemented a Bayesian Markov Chain Monte Carlo (MCMC) algorithm to infer what we call sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals. We use a family of birth-death models where individuals may remain in the tree process after the sampling, in particular we extend the birth-death skyline model [Stadler et al, 2013] to sampled ancestor trees. This method allows the detection of sampled ancestors as well as estimation of the probability that an individual will be removed from the process when it is sampled. We show that sampled ancestor birth-death models where all samples come from different time points are non-identifiable and thus require one parameter to be known in order to infer other parameters. We apply this method to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental epidemiological parameters. We also apply the method to infer divergence times and diversification rates when fossils are included among the species samples, so that fossilisation events are modelled as a part of the tree branching process. Such modelling has many advantages as argued in literature. The sampler is available as an open-source BEAST2 package (https://github.com/gavryushkina/sampled-ancestors).Comment: 34 pages (including Supporting Information), 8 figures, 1 table. Part of the work presented at Epidemics 2013 and The 18th Annual New Zealand Phylogenomics Meeting, 201

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation concepts

A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model -- also referred to as the fossilized birth-death (FBD) model -- gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects. However, the current mathematical treatment of this model does not allow for a group of temporally distinct fossil specimens to be assigned to the same species. In this paper, we provide a general mathematical FBD modeling framework that explicitly takes "stratigraphic ranges" into account, with a stratigraphic range being defined as the lineage interval associated with a single species, ranging through time from the first to the last fossil appearance of the species. To assign a sequence of fossil samples in the phylogenetic tree to the same species, i.e., to specify a stratigraphic range, we need to define the mode of speciation. We provide expressions to account for three common speciation modes: budding (or asymmetric) speciation, bifurcating (or symmetric) speciation, and anagenetic speciation. Our equations allow for flexible joint Bayesian analysis of paleontological and neontological data. Furthermore, our framework is directly applicable to epidemiology, where a stratigraphic range is the observed duration of infection of a single patient, "birth" via budding is transmission, "death" is recovery, and "sampling" is sequencing the pathogen of a patient. Thus, we present a model that allows for incorporation of multiple observations through time from a single patient

Bayesian total evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure

Closing the gap between palaeontological and neontological speciation and extinction rate estimates.

Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the "birth-death chronospecies" model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes

Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequencebased phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character set

ДЛИТЕЛЬНОСТЬ ГРАНИТОИДНОГО МАГМАТИЗМА ПЕРИФЕРИЧЕСКИХ ЧАСТЕЙ КРУПНЫХ ИЗВЕРЖЕННЫХ ПРОВИНЦИЙ (ПО ДАННЫМ 40AR/39 AR ИЗОТОПНЫХ ИССЛЕДОВАНИЙ ПЕРМОТРИАСОВЫХ ГРАНИТОИДОВ АЛТАЯ)

In large igneous provinces (LIP) of fold areas, granitoid rocks are dominant, while mantle-derivated rocks play a subordinate role in rock formation. If magma emissions are impulsive, it may take 25–30 million years for a LIP to form and take shape. In this paper, we present the results of 40Ar/39Ar isotopic studies of Permian-Triassic grani­toids in the Altai region, Russia, and clarify the evolution of this region located at the periphery of the Siberian LIP. These granitoids are very diverse and differ not only in their rock set, but also in the composition features. In the study region, the granodiorite-granite and granite-leucogranite association with the characteristics of I- and S-types as well rare metal ore-bearing leucogranites are observed along with gabbro- and syenite-granite series, including mafic and intermediate rocks with the A2-type geochemical features. The 40Ar/39Ar data obtained in our study suggest that most of the studied granitoids intruded within a short period of time, 254–247 Ma. This timeline is closely related to the formation of granitoids in theKuznetsk basin and dolerite dikes in the Terekta complex (251–248 and 255±5 Ma, respectively), as well as intrusions of lamproite and lamprophyre dikes of the Chuya complex (245–242 and 237–235 Ma). Thus, we conclude that the Altai Permian-Triassic granitoids are varied mainly due to the evolution of mafic magmatism.В складчатых областях крупные изверженные провинции (LIP) характеризуются резким преобладанием гранитоидов при подчиненной роли пород мантийного генезиса. Длительность формирования отдельных LIP может достигать 25–30 млн лет при импульсном характере магматизма. В работе конкретизируется схема формирования одного из периферических сегментов Сибирской LIP на основе 40Ar/39Ar изотопных исследований пермотриасовых гранитоидов Алтая, которые резко различны не только по набору пород, но и по особенностям их состава. Наряду с габбро- и сиенит-гранитными сериями, включающими основные и средние породы с геохимическими характеристиками пород A2-типа, на этом рубеже проявлены гранодиорит-гранитные и гранит-лейкогранитные ассоциации с характеристиками I- и S-типа, а также рудоносные редкометалльные лейкограниты. Результаты 40Ar/39Ar датирования свидетельствуют о том, что внедрение большинства изученных интрузий гранитоидов Айского, Теранжикского, Тархатинского, Белокурихинского и Синюшенского массивов, Точильненского и Осокинского штоков-сателлитов произошло в короткий промежуток времени – 254–247 млн лет. Фиксируется достаточно тесная временная связь формирования гранитоидов с формированием траппов Кузнецкого бассейна и долеритовых даек терехтинского комплекса (251–248 и 255±5 млн лет соответственно), с внедрением даек лампроитов и лампрофиров чуйского комплекса (245–242 и 237–235 млн лет). Таким образом, разнообразие пермотриасовых гранитоидов Алтая определяется, в первую очередь, эволюцией базитового магматизма

Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids

Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data—and doing this with rigor despite all the attendant challenges—is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species‐level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global‐scale analyses. We illustrate difficulties and opportunities using the rosids as a case study, arguing that assembly of biodiversity data that is scale‐appropriate—and therefore comprehensive and global in scope—is required to test global‐scale hypotheses. Synthesizing comprehensive biodiversity data sets in clades such as the rosids will be key to understanding the origin and present‐day evolutionary and ecological dynamics of the angiosperms.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143800/1/ajb21059.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143800/2/ajb21059_am.pd

The origin of animals: can molecular clocks and the fossil record be reconciled?

The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown-representatives of most animal phyla in the Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record. Critical assessment of both records may permit better resolution of the tempo and mode of early animal evolution.JAC and AGL acknowledge support from Natural Environment Research Council (NERC) Fellowships [grant numbers NE/J018325/1 and NE/L011409/1]. SB and JAC acknowledge funding from the Danish National Research Foundation [DNRF53] and the Swedish Research Council [2013-4290]. PCJD was supported by a Royal Society Wolfson Merit Award, a Leverhulme Trust Research Fellowship and a NERC standard grant [NE/F00348X/1]