Probabilistic Graphical Model Representation in Phylogenetics

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution

Estimating the duration of speciation from phylogenies

Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.</p

Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Funding: Funding information Austrian Science Fund, Grant/Award Number: P34524-B; Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/W000768/1; Deutsche Forschungsgemeinschaft, Grant/Award Number: HO 6201/1-1; Vienna Science and Technology Fund, Grant/Award Number: MA016-061.1. The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. 2. We implemented polymorphism-aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome-wide data. Simultaneously, PoMos can estimate mutation and selection biases. 3. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well-supported species tree, we found a mutation bias favouring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC-biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. 4. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes—for example, relaxed clock and divergence time estimation—offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification.Publisher PDFPeer reviewe

PM10- und PM2.5- Emissionspotentiale von Substraten der Tagebaue im Lausitzer Revier

Im Lausitzer Revier werden aktuell 4 Braukohlen-Tagebaue betrieben, die als Quellen für Feinstaub-Emissionen gelten und somit zur lokalen Luftbelastungen beitragen. Berechnungen von möglichen Zusatzbelastungen durch den Tagebaubetrieb ergaben jedoch große Differenzen zu Messungen der Behörden vor Ort. Die Ursachen hierfür liegen in der starren Handhabung von Emissionsfaktoren, die vor allem die durch Winderosion hervorgerufene flächenhafte Emission von PM10 und PM2.5 stark überschätzen. Die Substrate der Hauptarbeitsebenen aller Tagebaue wurden untersucht, um die Materialeigenschaften als auch die Oberflächeneigenschaften, die die Emissionen beeinflussen, zu charakterisieren. Im ersten Schritt wurde mittels Horizontal-Querstromsichtung das Emissionspotential aller Substrate im luftgetrockneten Zustand ermittelt. Hierbei wird bei einer Windgeschwindigkeit von 3 ms-1 das Probenmaterial am Anfang des Windkanals von oben zugeführt und durch die Schwerkraft und die horizontale Strömung nach Größe und aerodynamischen Eigenschaften über die 7 m lange Messstrecke sortiert. Am Ende des Windkanals erfolgte die Messung der Partikelgrößenverteilung der Staubfraktion. Einzelne Proben wurden behutsam rückbefeuchtet und ebenfalls auf diese Weise untersucht. Für Untersuchungen zum Einfluss der Winderosion auf die PM-Emissionen wurde die Messstrecke in voller Länge mit den Substraten befüllt und mit Windgeschwindigkeiten von 6, 8 und 10 ms-1 abgeblasen. Die abgetragene Sedimentmenge als auch die PM- Emissionen wurden am Ende der Messstrecke erfasst. Die Emissionspotentiale der Substrate nahmen in folgender Reihung ab: homogene Kohle &gt; homogene Feinsande &gt; heterogene Feinsande &gt; heterogene Grobsande &gt; heterogene (faserige) Kohle und lagen in den Bereichen 475 µgg-1 bis 22 µgg-1. Die Befeuchtung der sandigen Substrate auf ca. 2 M% erbrachte eine Reduzierung der PM-Emissionen um 95%, die der Kohle um 45%. Für die durch Winderosion ausgelösten PM-Emissionen ergab sich eine andere Reihenfolge der sandigen Substrate: Kohle &gt; heterogene Feinsande &gt; heterogene Grobsande &gt; homogene Feinsande. Hier wurden vor allem durch den Impakt saltierender Sandkörner Staubpartikel freigesetzt. Für jede der Windgeschwindigkeiten ergab sich über die Zeit eine maximale Abtrags- und PM-Emissionsrate. Wurde diese erreicht, blieb die Oberfläche stabil und es erfolgten keine weiteren PM-Emissionen

Posterior summarisation in Bayesian phylogenetics using Tracer 1.7

Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.status: publishe

Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors.

New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5-10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small-weighing 0.4 kg-and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends

Lessons learned from organizing and teaching virtual phylogenetics workshops

No abstract available

Diversity dynamics in New Caledonia: towards the end of the museum model?

<p>Abstract</p> <p>Background</p> <p>The high diversity of New Caledonia has traditionally been seen as a result of its Gondwanan origin, old age and long isolation under stable climatic conditions (the museum model). Under this scenario, we would expect species diversification to follow a constant rate model. Alternatively, if New Caledonia was completely submerged after its breakup from Gondwana, as geological evidence indicates, we would expect species diversification to show a characteristic slowdown over time according to a diversity-dependent model where species accumulation decreases as space is filled.</p> <p>Results</p> <p>We reanalyze available datasets for New Caledonia and reconstruct the phylogenies using standardized methodologies; we use two ultrametrization alternatives; and we take into account phylogenetic uncertainty as well as incomplete taxon sampling when conducting diversification rate constancy tests. Our results indicate that for 8 of the 9 available phylogenies, there is significant evidence for a diversification slowdown. For the youngest group under investigation, the apparent lack of evidence of a significant slowdown could be because we are still observing the early phase of a logistic growth (i.e. the clade may be too young to exhibit a change in diversification rates).</p> <p>Conclusions</p> <p>Our results are consistent with a diversity-dependent model of diversification in New Caledonia. In opposition to the museum model, our results provide additional evidence that original New Caledonian biodiversity was wiped out during the episode of submersion, providing an open and empty space facilitating evolutionary radiations.</p

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-