Abstract.-The paleontological record chronicles numerous episodes of mass extinction that 14 severely culled the Tree of Life. Biologists have long sought to assess the extent to which 15 these events may have impacted particular groups. We present a novel method for 16 detecting mass-extinction events from phylogenies estimated from molecular sequence data. 17We develop our approach in a Bayesian statistical framework, which enables us to harness 18 prior information on the frequency and magnitude of mass-extinction events. The approach 19 is based on an episodic stochastic-branching process model in which rates of speciation and 20 extinction are constant between rate-shift events. We model three types of events: (1) 21 instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in 22 extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events 23 is described by a separate compound Poisson process (CPP) model, where the waiting 24 times between each event are exponentially distributed with event-specific rate parameters. 25The magnitude of each event is drawn from an event-type specific prior distribution. 26 Parameters of the model are then estimated using a reversible-jump Markov chain Monte 27Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has 28 substantial power to detect the number of mass-extinction events, provides unbiased 29 estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., 30 below 5%) false discovery rate even in the case of background diversification rate variation. 31Finally, we provide an empirical application of this approach to conifers, which reveals that The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/020149 doi: bioRxiv preprint first posted online May. 31, 2015; The paleontological record documents numerous episodes of mass extinction that 40 severely culled the Tree of Life. As biologists, we often wish to assess whether these events 41 may have impacted particular groups. To this end, several statistical phylogenetic 42 approaches have been proposed to identify mass-extinction events from estimated 43 molecular phylogenies with divergence times, e.g., Nee et al. (1994) and Harvey et al. 44 (1994). These methods generally assume that the dated phylogeny is known without error, 45 and decompose the tree into a vector of waiting times between speciation events. Various 46 models of lineage diversification are then fit to these phylogenetic 'observations' using 47 maximum likelihood to estimate the speciation, b, and extinction, d, rates, and to identify 48 tree-wide shifts in diversification rate, including episodes of mass extinction. 60In order to distinguish more prosaic temporal variation in diversification rate from 61 bona fide mass-extinction events, we adopt a Bayesian statistical framework that enables us 62 to leverage prior information on the frequency and magnitude of mass-extinction events. 63Specifically, we d...

Grey mullets (Mugilidae, Ovalentariae) are coastal fishes found in near-shore environments of tropical, subtropical, and temperate regions within marine, brackish, and freshwater habitats throughout the world. This group is noteworthy both for the highly conserved morphology of its members-which complicates species identification and delimitation-and also for the uncommon herbivorous or detritivorous diet of most mullets. In this study, we first attempt to identify the number of mullet species, and then-for the resulting species-estimate a densely sampled time-calibrated phylogeny using three mitochondrial gene regions and three fossil calibrations. Our results identify two major subgroups of mullets that diverged in the Paleocene/Early Eocene, followed by an Eocene/Oligocene radiation across both tropical and subtropical habitats. We use this phylogeny to explore the evolution of feeding preference in mullets, which indicates multiple independent origins of both herbivorous and detritivorous diets within this group. We also explore correlations between feeding preference and other variables, including body size, habitat (marine, brackish, or freshwater), and geographic distribution (tropical, subtropical, or temperate). Our analyses reveal: (1) a positive correlation between trophic index and habitat (with herbivorous and/or detritivorous species predominantly occurring in marine habitats); (2) a negative correlation between trophic index and geographic distribution (with herbivorous species occurring predominantly in subtropical and temperate regions), and; (3) a negative correlation between body size and geographic distribution (with larger species occurring predominantly in subtropical and temperate regions). PLOS1/56 1 Grey mullets (Mugilidae, Ovalentariae) occur in coastal waters worldwide 2 and represent an important food source in several European and Pacific 3 countries. Mugilids are geographically widespread, with species ranging 4 from the tropics to northern Europe, and vary greatly in body size, with 5 species ranging from 10 − 120 cm in total length (TL). Despite this 6 variation, the morphology of mullets is extremely conservative; all species 7 share a torpedo-shaped body form with a similar overall appearance, 8 which makes accurate species identification exceptionally challenging [1]. 9 Most mullet species are euryhaline and may spend at least part of their 10 life cycle in brackish or freshwater habitats, even though the majority of 11 the adult life-stage and reproduction typically occur in marine habitats. 12 However, a few species (e.g., Liza abu, Agonostomus monticula and A. 13 catalai) are exclusively freshwater [1-4]. 14 The diet of grey mullets is unusual among marine fishes: most mullet 15 species feed predominantly on food items-such as detritus and 16 filamentous algae-with relatively low calories and/or protein per unit 17 mass (i.e., "low-quality food resources" [5]). Mullets have evolved a 18 number of morphological adaptations associated with this diet, including 19 a stomach with...

We performed phylodynamic analyses of all available SARS-CoV-2 genomes from the early phase of the COVID-19 pandemic---combined with a novel dataset on contemporary global air-travel volume---to assess the efficacy of public-health measures on viral geographic spread. Globally, viral dispersal rates are significantly correlated with air-travel volume, and widespread international air-travel bans imposed against China by early February coincide with a significant reduction in geographic viral spread. In North America, the efficacy of this travel ban was temporary, possibly due to the lack of both containment measures against other infected regions and domestic mitigation measures. By contrast, in China, domestic mitigation measures were correlated with a long-term reduction in viral spread, despite repeated international introductions. Our study supports a role for both targeted international containment and domestic mitigation measures as critical components of a more comprehensive public-health strategy to mitigate future outbreaks caused by the emergence of novel SARS-CoV-2 variants.