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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
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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.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
One of the main explanations for the stunning diversity of teleost fishes (approximately 29,000 species, nearly half of all vertebrates) is that a fish-specific whole-genome duplication event (FSGD) ...in the ancestor to teleosts triggered their subsequent radiation. However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested.
Here we show that one of three major diversification rate shifts within ray-finned fishes occurred at the base of the teleost radiation, as predicted by the FSGD hypothesis. We also find evidence for two rate increases that are much younger than the inferred age of the FSGD: one in the common ancestor of most ostariophysan fishes, and a second one in the common ancestor of percomorphs. The biodiversity contained within these two clades accounts for more than 88% of living fish species.
Teleosts diversified explosively in their early history and this burst of diversification may have been caused by genome duplication. However, the FSGD itself may be responsible for a little over 10% of living teleost biodiversity. ~88% of species diversity is derived from two relatively recent radiations of freshwater and marine fishes where genome duplication is not suspected. Genome duplications are a common event on the tree of life and have been implicated in the diversification of major clades like flowering plants, vertebrates, and gnathostomes. However our results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aim: Capuchin monkey species are widely distributed across Central and South America. Morphological studies consistently divide the clade into robust and gracile forms, which show extensive sympatry ...in the Amazon Basin. We use genetic data to test whether Miocene or Plio-Pleistocene processes may explain capuchin species' present distributions, and consider three possible scenarios to explain widespread sympatry. Location: The Neotropics, including the Amazon and Atlantic Coastal Forest. Methods: We sequenced the 12S ribosomal RNA and cytochrome b genes from capuchin monkey specimens. The majority were sampled from US museum collections and were wild-caught individuals of known provenance across their distribution. We applied a Bayesian discrete-states diffusion model, which reconstructed the most probable history of invasion across nine subregions. We used comparative methods to test for phylogeographic association and dispersal rate variation. Results: Capuchins contained two well supported monophyletic clades, the morphologically distinct 'gracile' and 'robust' groups. The time-tree analysis estimated a late Miocene divergence between Cebus and Sapajus and a subsequent Plio-Pleistocene diversification within each of the two clades. Bayesian analysis of phylogeographic diffusion history indicated that the current wide-ranging sympatry of Cebus and Sapajus across much of the Amazon Basin was the result of a single explosive late Pleistocene invasion of Sapajus from the Atlantic Forest into the Amazon, where Sapajus is now sympatric with gracile capuchins across much of their range. Main conclusions: The biogeographic history of capuchins suggests late Miocene geographic isolation of the gracile and robust forms. Each form diversified independently, but during the Pleistocene, the robust Sapajus expanded its range from the Atlantic Forest to the Amazon, where it has now encroached substantially upon what was previously the exclusive range of gracile Cebus. The genus Cebus, as currently recognized, should be split into two genera to reflect the Miocene divergence and two subsequent independent Pliocene radiations: Cebus from the Amazon and Sapajus from the Atlantic Forest.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
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.
Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species ...richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.
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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.
Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage ...in phylogenetic data; however, accessing and reusing these data remain challenging.
We introduce the Fish Tree of Life website and associated r package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the r package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyse the data.
We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the r package. First, we test for the presence of long branch attraction artefacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package.
This resource makes a large comparative vertebrate dataset easily accessible via the website, while the r package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other r packages and software for molecular biology and comparative methods.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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