Jason T. Weir

GEIGER: investigating evolutionary radiations

SUMMARY GEIGER is a new software package, written in the R language, to describe evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGERs simulation algorithms can be used to analyze the statistical power of comparative approaches. AVAILABILITY 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/.

Calibrating the avian molecular clock

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.

Early bursts of body size and shape evolution are rare in comparative data.

George Gaylord Simpson famously postulated that much of lifes 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.

The latitudinal gradient in recent speciation and extinction rates of birds and mammals.

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 others 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.

Divergent Timing and Patterns of Species Accumulation in Lowland and Highland Neotropical Birds

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.

Ice sheets promote speciation in boreal birds

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.

The Great American Biotic Interchange in birds.

The sudden exchange of mammals over the land bridge between the previously isolated continents of North and South America is among the most celebrated events in the faunal history of the New World. This exchange resulted in the rapid merging of continental mammalian faunas that had evolved in almost complete isolation from each other for tens of millions of years. Yet, the wider importance of land bridge-mediated interchange to faunal mixing in other groups is poorly known because of the incompleteness of the fossil record. In particular, the ability of birds to fly may have rendered a land bridge unnecessary for faunal merging. Using molecular dating of the unique bird faunas of the two continents, we show that rates of interchange increased dramatically after land bridge completion in tropical forest-specializing groups, which rarely colonize oceanic islands and have poor dispersal abilities across water barriers, but not in groups comprised of habitat generalists. These results support the role of the land bridge in the merging of the tropical forest faunas of North and South America. In contrast to mammals, the direction of traffic across the land bridge in birds was primarily south to north. The event transformed the tropical avifauna of the New World.

Sexual selection accelerates signal evolution during speciation in birds

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.

Limits to speciation inferred from times to secondary sympatry and ages of hybridizing species along a latitudinal gradient.

Range expansions are critical to renewed bouts of allopatric or parapatric speciation. Limits on range expansions—and, by implication, speciation—include dispersal ability and permeability of geographical barriers. In addition, recently diverged taxa may interfere with each other, preventing mutual expansion of each other’s range into sympatry, because reproductive isolation is incomplete and/or ecological competition particularly strong. On the basis of geographical distributions and mitochondrial DNA phylogenetic information for 418 recently diverged species of New World birds, we estimate that secondary sympatry takes on the order of millions of years following population splitting and hence could impose an important limit on the rate of range expansion, thereby limiting further rounds of species formation. Average rates of achievement of sympatry have been faster in the temperate region (we estimate 1.7 million years to sympatry at 60°) than in the tropics (3.2 million years to sympatry at the equator). Evidence from the ages of species with hybrid zones implies that one factor associated with the slowed sympatry in the tropics is the rate of accumulation of reproductive isolation.

Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.