Irby J. Lovette

Explosive Evolutionary Radiations: Decreasing Speciation or Increasing Extinction Through Time?

Abstract A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such “explosive-early” diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, “explosive early” patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.

Density-dependent diversification in North American wood warblers

Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.

Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. ‘beetles’), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australias most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.

Explosive speciation in the New World Dendroica warblers

The 27 species of Dendroica wood-warblers represent North Americas most spectacular avian adaptive radiation. Dendroica species exhibit high levels of local sympatry and differ in plumage and song, but the group contrasts with other well–known avian adaptive radiations such as the Hawaiian honeycreepers and Galapagos finches in that Dendroica species have differentiated modestly in morphometric traits related to foraging. Instead, sympatric Dendroica tend to partition resources behaviourally and they have become a widely cited example of competitive exclusion. We explored the temporal structure of Dendroica diversification via a phylogeny based on 3639 nucleotides of protein–coding mitochondrial DNA (mtDNA). The taxa sampled included 60 individuals representing 24 Dendroica species and a variety of other paruline warbler and outgroup species. Mitochondrial divergences among Dendroica species were generally large (mean pairwise interspecific distances, 10.0%) and many species were rooted in a basal polytomy. The prevalence of long terminal branches indicates that these species have evolved efficient isolating mechanisms that have prevented mtDNA introgression despite the many opportunities for hybridization resulting from local sympatry. Comparisons with a null model of random bifurcation–extinction demonstrate that cladogenesis in Dendroica has been clustered non–randomly with respect to time, with a significant burst of speciation occurring early in the history of the genus, possibly as long ago as the Late Miocene or Early Pliocene periods. Although this non–random clustering of speciation is consistent with the pattern expected of an adaptive radiation, the age of the Dendroica radiation suggests it is an ‘ancient species flock’ in which most extant species represent lineages that have long been evolutionarily independent.

Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida scrub‐jay (Aphelocoma cœrulescens)

The delimitation of populations, defined as groups of individuals linked by gene flow, is possible by the analysis of genetic markers and also by spatial models based on dispersal probabilities across a landscape. We combined these two complimentary methods to define the spatial pattern of genetic structure among remaining populations of the threatened Florida scrub‐jay, a species for which dispersal ability is unusually well‐characterized. The range‐wide population was intensively censused in the 1990s, and a metapopulation model defined population boundaries based on predicted dispersal‐mediated demographic connectivity. We subjected genotypes from more than 1000 individual jays screened at 20 microsatellite loci to two Bayesian clustering methods. We describe a consensus method for identifying common features across many replicated clustering runs. Ten genetically differentiated groups exist across the present‐day range of the Florida scrub‐jay. These groups are largely consistent with the dispersal‐defined metapopulations, which assume very limited dispersal ability. Some genetic groups comprise more than one metapopulation, likely because these genetically similar metapopulations were sundered only recently by habitat alteration. The combined reconstructions of population structure based on genetics and dispersal‐mediated demographic connectivity provide a robust depiction of the current genetic and demographic organization of this species, reflecting past and present levels of dispersal among occupied habitat patches. The differentiation of populations into 10 genetic groups adds urgency to management efforts aimed at preserving what remains of genetic variation in this dwindling species, by maintaining viable populations of all genetically differentiated and geographically isolated populations.

SIMULTANEOUS EFFECTS OF PHYLOGENETIC NICHE CONSERVATISM AND COMPETITION ON AVIAN COMMUNITY STRUCTURE

We currently have only a partial understanding of how phylogenetic relationships relate to patterns of community structure, in part because, for most groups of organisms, we do not know the extent to which ecological similarity results from common ancestry. Associations between phylogenetic relatedness and local community structure are particularly interesting for groups in which many species that span a gradient of phylogenetic divergence occur in potential sympatry. We explored the relationship between evolutionary relatedness and current species co-occurrence among the North American wood-warblers (Aves: Parulidae), a group of songbirds known both for its species diversity and for exhibiting high levels of sympatry at breeding sites. Species co-occurrences were derived from North American Breeding Bird Survey transects comprising 160,000 census points distributed across North America. The nested point-within-transect structure of this survey provides an unusual opportunity to remove larger-scale geographical effects on local community composition and thereby consider patterns of co-occurrence only among regionally sympatric pairs of species. We indexed evolutionary relatedness among all pairs of taxa by genetic distances based on long mitochondrial DNA protein-coding sequences. Most regionally sympatric taxon pairs rarely co-occur at local sites, and the most closely related never exhibit high local co-occurrences, as predicted if past or present competitive effects are strongest for these recently separated lineages. Quantile regression shows that, for a subset of taxa, local co-occurrence does increase with time since common ancestry, and that this apparent relaxation of competitive exclusion is strongest for distantly related species that have differentiated in fundamental ecological and behavioral traits, such as terrestrial vs. arboreal foraging. Comparisons against a null model of species co-occurrence further demonstrate that these patterns occur against a background of phylogenetic niche conservatism: across all phylogenetic distances, sympatric species co-occurred at higher rates than expected by chance, a pattern that might stem from a tendency by these species to show conservatism in their selection of similar general habitat types. Considered in concert, these analyses suggest the simultaneous mediation of local community structure by the ecological similarity of closely related species and by trait divergence among a subset of more distant lineages.

Fifty-Second Supplement to the American Ornithologists' Union check-list of North American Birds

The Auk, Vol. 128, Number 3, pages 600−613. ISSN 0004-8038, electronic ISSN 1938-4254.  2011 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2011.128.3.600 R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11

Going to Extremes: Contrasting Rates of Diversification in a Recent Radiation of New World Passerine Birds

Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World that comprises ~8% of all bird species, may be the true driver of this rate increase. Understanding the patterns and processes of diversification of this diverse lineage may go a long way toward explaining the apparently rapid diversification rates of both passerines and of birds as a whole. We present the first multilocus phylogenetic analyses of this endemic New World radiation of finch relatives that include sampling of all recognized genera, a relaxed molecular clock analysis of its divergence history, and an analysis of its broad-scale diversification patterns. These analyses recovered 5 major lineages traditionally recognized as avian families, but identified an additional 10 relatively ancient lineages worthy of recognition at the family level. Time-calibrated diversification analyses suggested that at least 3 of the 15 family-level lineages were significantly species poor given the entire groups background diversification rate, whereas at least one-the tanagers of family Thraupidae-appeared significantly more diverse. Lack of an age-diversity relationship within this clade suggests that, due to rapid initial speciation, it may have experienced density-dependent ecological limits on its overall diversity.

Analysis and visualization of complex Macroevolutionary dynamics: An example from Australian Scincid lizards

The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+scincid lizards that constitute Australias most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; >90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees. [Bayesian; diversification; evolvability; lizard; macroevolution, punctuated equilibrium, speciation.].

Syllable type consistency is related to age, social status and reproductive success in the tropical mockingbird

Many animals repeat standardized displays multiple times while attracting a mate or deterring a rival. In such contexts it is possible that the ability to perform each display or signal type in a consistent fashion is under direct selection. Studies on sexual selection on song learning in birds have focused on differences in repertoire size with less attention to the potential importance of being able to perform each song/syllable type with high consistency. We present evidence that tropical mockingbirds decrease the variation between renditions of each syllable type as they grow older (i.e., become more consistent) and that more consistent males in this species tend to have higher dominance status and reproductive success. These findings stress the importance of consistency in the performance of sexual displays and suggest that this parameter may be very relevant even in species that are selected for high vocal diversity (i.e., large repertoires). In addition to signalling dominance status and age, we hypothesize that syllable type consistency may also be an indicator of the integrity of brain function in birds analogous to the tests used for neuropsychological assessment in humans.