Proceedings of the National Academy of Sciences · 2019 · 404 citations · 87 references
Life SciencesBiologyEvolutionary BiologyPaleoanthropologyPaleoecologyPhylogeneticsBird EvolutionDiversification RatesLineage DivergenceMacroevolutionary PatternsSpecies DiversificationVertebrate EvolutionAvian PhylogenyCenozoic Avian EvolutionCenozoic DiversificationContinental GlaciationFossil-based Diversification EstimatesFossil-calibrated DiversificationOrigin Of BirdsRates Of Evolutionary Diversification
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
87
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred Grabherr, Brian J. Haas, Moran Yassour et al. · Nature Biotechnology · 2011 · 22.6K citations · Full text
Robert E. Kass, Adrian E. Raftery · Journal of the American Statistical Association · 1995 · 12.3K citations
Natural Sciences, Behavioral Sciences, Bayesian Biostatistics +11
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Alexei J. Drummond, Marc A. Suchard, Dong Xie et al. · Molecular Biology and Evolution · 2012 · 10.4K citations · Full text
The global diversity of birds in space and time
Walter Jetz, Gavin H. Thomas, Jeffrey B. Joy et al. · Nature · 2012 · 4K citations · Full text
Life Sciences, Biology, Ecology +12