Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.

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.

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1287 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

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An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.

High tropical species diversity is often attributed to evolutionary dynamics over long timescales. It is possible, however, that latitudinal variation in diversification begins when divergence occurs within species. Phylogeographic data capture this initial stage of diversification in which populations become geographically isolated and begin to differentiate genetically. There is limited understanding of the broader implications of intraspecific diversification because comparative analyses have focused on species inhabiting and evolving in restricted regions and environments. Here, we scale comparative phylogeography up to the hemisphere level and examine whether the processes driving latitudinal differences in species diversity are also evident within species. We collected genetic data for 210 New World bird species distributed across a broad latitudinal gradient and estimated a suite of metrics characterizing phylogeographic history. We found that lower latitude species had, on average, greater phylogeographic diversity than higher latitude species and that intraspecific diversity showed evidence of greater persistence in the tropics. Factors associated with species ecologies, life histories, and habitats explained little of the variation in phylogeographic structure across the latitudinal gradient. Our results suggest that the latitudinal gradient in species richness originates, at least partly, from population-level processes within species and are consistent with hypotheses implicating age and environmental stability in the formation of diversity gradients. Comparative phylogeographic analyses scaled up to large geographic regions and hundreds of species can show connections between population-level processes and broad-scale species-richness patterns.

The acceptance of the generalized or unified concept of species (i.e. that species are segments of population lineages) implies that an important task for systematists is to focus on identifying lineages and on testing hypotheses about the acquisition of properties such as phenotypic diagnosability, reciprocal monophyly, or mechanisms of reproductive isolation. However, delimiting species objectively remains one of the most challenging problems faced by biologists. In the present study, we begin to tackle the thorny issue of species delimitation in a complicated group of Neotropical passerine birds (the Arremon torquatus complex, Emberizidae) in which sets of characters vary substantially across space, but do not obviously vary in a concerted fashion. To earlier discussions of species limits in the group, we add a historical perspective offered by a recent molecular phylogeny, present quantitative analyses of morphological and vocal variation, and incorporate ecological niche models as a new tool that aids species delimitation by highlighting cases of ecological distinctiveness and cases where populations appear to be in independent evolutionary trajectories, despite being connected by environments unlikely to represent barriers to gene flow. We demonstrate that at least one pair of taxa (and likely another) currently treated as conspecific are, in fact, distinct lineages that merit species status under essentially any species criterion. However, other pairwise comparisons are not as straightforward owing to nonconcordant patterns of variation in different traits and to the impossibility of distinguishing which characters are causes and which are consequences of reproductive (and evolutionary) isolation. After considering several alternatives, we propose a provisional classification of the complex recognizing eight tentative species-level taxa. Although this classification is likely to change as more detailed work is conducted, it provides a better foundation for studying the biology of these birds and helps to better describe their diversity, which is obscured when all taxa are subsumed into a single species name. The present study highlights several outstanding challenges, both practical and conceptual, for future studies.

Aim  To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location  Humid forests of the Neotropical region. Methods  We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein‐coding mitochondrial gene sequences. Phylogenetic relationships were inferred using Bayesian and maximum‐likelihood methods. We used Bayesian coalescent‐based approaches to evaluate demographic changes through time, and to estimate the timing of diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage‐through‐time plots. Results  The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor–Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene. Main conclusions  Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest‐dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species.