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

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

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

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

ТЕРМОХРОНОЛОГИЯ И МАТЕМАТИЧЕСКОЕ МОДЕЛИРОВАНИЕ ДИНАМИКИ ФОРМИРОВАНИЯ РЕДКОМЕТАЛЛЬНО‐ГРАНИТНЫХ МЕСТОРОЖДЕНИЙ АЛТАЙСКОЙ КОЛЛИЗИОННОЙ СИСТЕМЫ

The article presents an event correlation of the Permian‐Triassic granites of the Altai collision system, which are associated with industrial ore deposits and occurrences (Mo‐W, Sn‐W, Li‐Ta‐Be). The multi‐system and multi‐mineral isotope datings of igneous rocks and ore bodies (U/Pb, Re/Os, Rb/Sr, Ar/Ar‐methods) suggest the postcollisional (intraplate) formation of ore‐magmatic systems (OMS), the duration of which depended on the crustmantle interaction and the rates of tectonic exposure of geoblocks to the upper crustal levels.Two cases of the OMS thermal history are described: (1) Kalguty Mo‐W deposit associated with rare‐metal granite‐leucogranites and ongonite‐ elvan dykes, and (2) Novo‐Akhmirov Li‐Ta deposit represented by topaz‐zinnwaldite granites and the contemporary lamprophyre and ongonit‐elvan dykes. For these geological objects, numerical modeling was carried out. The proposed models show thermal cooling of the deep magmatic chambers of granite composition, resulting in the residual foci of rare‐metal‐granite melts, which are known as the petrological indicators of industrial ore deposits (Mo‐W, Sn‐W, Li‐Ta‐Be). According to the simulation results concerning the framework of a closed magmatic system with a complex multistage development history, the magmatic chamber has a lower underlying observable massif and a reservoir associated with it. A long‐term magmatic differentiation of the parental melt (a source of rare‐metal‐granite melts and ore hydrothermal fluids) takes place in this reservoir.В статье проведена событийная корреляция пермотриасовых гранитов Алтайской коллизионной системы, с которыми связаны промышленные месторождения и рудопроявления (Mo‐W, Sn‐W, Li‐Ta‐Be). Мультисистемное и мультиминеральное изотопное датирование магматических пород и рудных тел (U/Pb, Re/Os, Rb/Sr, 40Ar/39Ar – методы) указывает на постколлизионное (внутриплитное) формирование рудно‐ магматических систем, длительность существования которых зависела от корово‐мантийного взаимодействия и скорости тектонического экспонирования геоблоков на верхние уровни земной коры. Рассмотрены термические истории двух РМС: 1) Калгутинского Mo‐W месторождения, связанного с редкометалльными гранит‐лейкогранитами и онгонит‐эльвановыми дайками, 2) Ново‐Ахмировского Li‐Ta месторождения, пред‐ ставленного топаз‐циннвальдитовыми гранитами, и связанными с ним во времени лампрофирами и онгонит‐эльвановыми дайками. Для этих геологических объектов проведено численное моделирование и построены модели термического остывания глубинных магматических камер гранитного состава, приводящие к остаточным очагам редкометалльно‐гранитных расплавов – петрологических индикаторов промышленных месторождений (Mo‐W, Sn‐W, Li‐Ta‐Be). Результаты моделирования показывают, что в рамках замкнутой системы со сложной многостадийной историей должен существовать нижний, подстилающий магматический резервуар. В этом резервуаре происходит длительная дифференциация родоначальной магмы, которая является источником редкометалльно‐гранитных остаточных расплавов и рудных гидротермальных флюидов

BEAST 2.5:An advanced software platform for Bayesian evolutionary analysis

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release

DURATION OF GRANITOID MAGMATISM IN PERIPHERAL PARTS OF LARGE IGNEOUS PROVINCES (BASED ON 40AR/39AR ISOTOPIC STUDIES OF ALTAI PERMIAN-TRIASSIC GRANITOIDS)

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