A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements

Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 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. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. 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

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

<p>Abstract</p> <p>Background</p> <p>One of the main explanations for the stunning diversity of teleost fishes (~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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

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.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/1/mee313182-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/2/mee313182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/3/mee313182.pd

Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes

The ability to sustain high swimming speeds is believed to be an important factor affecting resource acquisition in fishes. While we have gained insights into how fin morphology and motion influences swimming performance in coral reef fishes, the role of other traits, such as body shape, remains poorly understood. We explore the ability of two mechanistic models of the causal relationship between body fineness ratio and endurance swimming-performance to predict maximum prolonged-swimming speed (Umax ) among 84 fish species from the Great Barrier Reef, Australia. A drag model, based on semi-empirical data on the drag of rigid, submerged bodies of revolution, was applied to species that employ pectoral-fin propulsion with a rigid body at U max. An alternative model, based on the results of computer simulations of optimal shape in self-propelled undulating bodies, was applied to the species that swim by body-caudal-fin propulsion at Umax . For pectoral-fin swimmers, Umax increased with fineness, and the rate of increase decreased with fineness, as predicted by the drag model. While the mechanistic and statistical models of the relationship between fineness and Umax were very similar, the mechanistic (and statistical) model explained only a small fraction of the variance in Umax . For body-caudal-fin swimmers, we found a non-linear relationship between fineness and Umax , which was largely negative over most of the range of fineness. This pattern fails to support either predictions from the computational models or standard functional interpretations of body shape variation in fishes. Our results suggest that the widespread hypothesis that a more optimal fineness increases endurance-swimming performance via reduced drag should be limited to fishes that swim with rigid bodies.MEA was partially supported by National Science Foundation Division of Environmental Biology (NSF DEB) grant 0842397 (http://www.nsf.gov/div/ index.jsp?div = DEB). CJF was partially supported by the Australian Research Council (http://www.arc.gov.au/)

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?

<p>Abstract</p> <p>Background</p> <p>Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes.</p> <p>Results</p> <p>Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications.</p> <p>Conclusion</p> <p>The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within <it>Scarus </it>and <it>Chlorurus</it>. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification.</p