This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad‐scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early‐burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long‐term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

Although the tropics harbor greater numbers of species than do temperate zones, it is not known whether the rates of speciation and extinction also follow a latitudinal gradient. By sampling birds and mammals, we found that the distribution of the evolutionary ages of sister species-pairs of species in which each is the other's closest relative-adheres to a latitudinal gradient. The time to divergence for sister species is shorter at high latitudes and longer in the tropics. Birth-death models fitting these data estimate that the highest recent speciation and extinction rates occur at high latitudes and decline toward the tropics. These results conflict with the prevailing view that links high tropical diversity to elevated tropical speciation rates. Instead, our findings suggest that faster turnover at high latitudes contributes to the latitudinal diversity gradient.

Molecular clocks are widely used to date phylogenetic events, yet evidence supporting the rate constancy of molecular clocks through time and across taxonomic lineages is weak. Here, we present 90 candidate avian clock calibrations obtained from fossils and biogeographical events. Cross-validation techniques were used to identify and discard 16 inconsistent calibration points. Molecular evolution occurred in an approximately clock-like manner through time for the remaining 74 calibrations of the mitochondrial gene, cytochrome b. A molecular rate of approximately 2.1% (+/- 0.1%, 95% confidence interval) was maintained over a 12-million-year interval and across most of 12 taxonomic orders. Minor but significant variance in rates occurred across lineages but was not explained by differences in generation time, body size or latitudinal distribution as previously suggested.

The premise that Pleistocene ice ages played an important role in generating present-day species diversity has been challenged by genetic data indicating that most of the youngest terrestrial species on Earth coalesced long before major glacial advances. However, study has been biased towards faunas distributed at low latitudes that were not directly fragmented by advancing ice sheets. Using mitochondrial sequence divergence and a molecular clock, we compared the coalescence times of pairs of avian species belonging to superspecies complexes from the high-latitude boreal forest with those of sub-boreal and tropical avifaunas of the New World. Remarkably, all coalescence events in boreal superspecies date to the Pleistocene, providing direct evidence that speciation was commonly initiated during recent glacial periods. A pattern of endemism in boreal superspecies plausibly links the timing of divergence to the fragmentation of the boreal forest by ice sheets during the Mid- and Late Pleistocene. In contrast to the boreal superspecies, only 56% of sub-boreal and 46% of tropical superspecies members coalesced during the Pleistocene, suggesting that avifaunas directly fragmented by ice sheets experienced rapid rates of diversification, whereas those distributed farther south were affected to a lesser extent. One explanation for the absence of pre-Pleistocene superspecies in boreal avifaunas is that strong selection pressures operated in boreal refugia, causing superspecies members to achieve ecological differentiation at an accelerated rate.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Abstract. Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.

Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male–male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation.