Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this ...vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. ...The pufferfishes (family Tetraodon‐tidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological opportunity for adaptive radiation, and thus provide a unique system for testing the hypothesis that shifts to new habitats alter diversification rates. To test this hypothesis, we sequenced eight genes for 96 species of pufferfishes and closely related porcupine fishes, and added 19 species from sequences available in GenBank. We time‐calibrated the molecular phylogeny using three fossils, and performed several comparative analyses to test whether colonization of novel habitats led to shifts in the rate of speciation and body size evolution, central predictions of clades experiencing ecological adaptive radiation. Colonization of freshwater is associated with lower rates of cladogenesis in pufferfishes, although these lineages also exhibit accelerated rates of body size evolution. Increased rates of cladogenesis are associated with transitions to coral reefs, but reef lineages surprisingly exhibit significantly lower rates of body size evolution. These results suggest that ecological opportunity afforded by novel habitats may be limited for pufferfishes due to competition with other species, constraints relating to pufferfish life history and trophic ecology, and other factors.
During the formation of synapses, specific regions of pre- and postsynaptic cells associate to form a single functional transmission unit. In this process, synaptogenic factors are necessary to ...modulate pre- and postsynaptic differentiation. In mammals, different Wnt ligands operate through canonical and non-canonical Wnt pathways, and their precise functions to coordinate synapse structure and function in the mature central nervous system are still largely unknown. Here, we studied the effect of different Wnt ligands on postsynaptic organization. We found that Wnt-5a induces short term changes in the clustering of PSD-95, without affecting its total levels. Wnt-5a promotes the recruitment of PSD-95 from a diffuse dendritic cytoplasmic pool to form new PSD-95 clusters in dendritic spines. Moreover, Wnt-5a acting as a non-canonical ligand regulates PSD-95 distribution through a JNK-dependent signaling pathway, as demonstrated by using the TAT-TI-JIP peptide in mature hippocampal neurons. Finally, using adult rat hippocampal slices, we found that Wnt-5a modulates glutamatergic synaptic transmission through a postsynaptic mechanism. Our studies indicate that the Wnt-5a/JNK pathway modulates the postsynaptic region of mammalian synapse directing the clustering and distribution of the physiologically relevant scaffold protein, PSD-95.
Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite ...the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that ...diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on “sampling fractions” can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with lowoverall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases.We showthat stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates.We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees TACT) that uses birth–death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of ...plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.
Growing evidence indicates that Wingless-type (Wnt) signaling plays an important role in the maturation of the central nervous system. We report here that Wingless-type family member 5A (Wnt-5a) is ...expressed early in development and stimulates dendrite spine morphogenesis, inducing de novo formation of spines and increasing the size of the preexisting ones in hippocampal neurons. Wnt-5a increased intracellular calcium concentration in dendritic processes and the amplitude of NMDA spontaneous miniature currents. Acute application of Wnt-5a increased the amplitude of field excitatory postsynaptic potentials (fEPSP) in hippocampal slices, an effect that was prevented by calcium-channel blockers. The physiological relevance of our findings is supported by studies showing that Wnt scavengers decreased spine density, miniature excitatory postsynaptic currents, and fEPSP amplitude. We conclude that Wnt-5a stimulates different aspects of synaptic differentiation and plasticity in the mammalian central nervous system.
Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many ...existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package.
mwpennell@gmail.com
Supplementary data are available at Bioinformatics online.
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•Lineages of Cacajao, Cebus and Callicebus on opposite banks of Rio Negro show spatiotemporal concordance of diversification.•Our results support a Pleistocene origin for Rio ...Negro.•The Rio Branco was a physical boundary to six primate genera.•The role of Rio Branco as a vicariant agent for primates could not be confirmed.
The role of Amazonian rivers as drivers of speciation through vicariance remains controversial. Here we explore the riverine hypothesis by comparing spatial and temporal concordances in pattern of diversification for all diurnal primates of Rio Negro and its largest tributary, Rio Branco. We built a comprehensive comparative phylogenetic timetree to identify sister lineages of primates based on mitochondrial cytochrome b DNA sequences from 94 samples, including 19 of the 20 species of diurnal primates from our study region and 17 related taxa from elsewhere. Of the ten primate genera found in this region, three had populations on opposite banks of Rio Negro that formed reciprocally monophyletic clades, with roughly similar divergence times (Cebus: 1.85Ma, HPD 95% 1.19–2.62; Callicebus: 0.83Ma HPD 95% 0.36–1.32, Cacajao: 1.09Ma, 95% HPD 0.58–1.77). This also coincided with time of divergence of several allopatric species of Amazonian birds separated by this river as reported by other authors. Our data offer support for the riverine hypothesis and for a Plio-Pleistocene time of origin for Amazonian drainage system. We showed that Rio Branco was an important geographical barrier, limiting the distribution of six primate genera: Cacajao, Callicebus, Cebus to the west and Pithecia, Saguinus, Sapajus to the east. The role of this river as a vicariant agent however, was less clear. For example, Chiropotes sagulata on the left bank of the Rio Branco formed a clade with C. chiropotes from the Amazonas Department of Venezuela, north of Rio Branco headwaters, with C. israelita on the right bank of the Rio Branco as the sister taxon to C. chiropotes+C. sagulata. Although we showed that the formation of the Rio Negro was important in driving diversification in some of our studied taxa, future studies including more extensive sampling of markers across the genome would help determine what processes contributed to the evolutionary history of the remaining primate genera.
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium ...proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.
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