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The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace’s Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace’s Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level data set of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group’s historical biogeography and the effects of the biogeographic barriers on their macroevolutionary dynamics. The tree is well resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace’s Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier was generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea’s central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace’s Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace’s Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification. [Historical biogeography; island biogeography; Melanesia; molecular phylogenetics; state-dependent diversification and extinction.]

Birds-of-paradise represent a textbook example for geographical speciation and sexual selection. Perhaps the most iconic genus is Paradisaea, which is restricted to New Guinea and a few surrounding islands. Although several species concepts have been applied in the past to disentangle the different entities within this genus, no attempt has been made so far to uncover phylogeographical patterns based on a genetic dataset that includes multiple individuals per species. Here, we applied amplicon sequencing for the mitochondrial fragment Cytb for a total of 69 museum specimens representing all seven Paradisaea species described and inferred both phylogenetic relationships and colonization pathways across the island. Our analyses show that the most recent common ancestor of the diverging lineages within Paradisaea probably originated in the Late Miocene in the eastern part of the Central Range and suggest that tectonic processes played a key role in shaping the diversification and distribution of species. All species were recovered as monophyletic, except for those within the apoda–minor–raggiana clade, which comprises the allopatric and parapatric species P. apoda, P. minor and P. raggiana. The comparatively young divergence times, together with possible instances of mitochondrial introgression and incomplete lineage sorting, suggest recent speciation in this clade.

The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya.

The continued use of the idea of homology is questionable on philosophical and scientific grounds. It is based on the widespread idea that a "homologue" in extant taxa can be "traced back" to a feature in common ancestor. In contrast, Richard Owen, who first used the term in 1846, saw homology (homologue) differently, as "sameness": "the same organ in different animals under every variety of form and function." At that point in time, he was not influenced by evolutionary thinking, and more focused on the details and approaches to biological comparison and description. His was a perceptive approach to comparison. This paper argues that the concept of homology no longer plays a useful role in comparative biology. It is a conceptual idea with little or no empirical implications for modern comparisons among phenotypes. Comparative biology now uses formal phylogenetic analysis in which similar features in individuals of two or more taxa are treated as characters on a tree and tested for historical "sameness" in terms of the concept of synapomorphy. If we are to understand the complexities of phenotypic evolution, applying this method to detailed comparative data will be essential. At the same time, a deep understanding of the phenotype and its history will emerge only through the use of multidisciplinary approaches that address historical changes at different hierarchical levels.

Joel Cracraft introduces the Hoatzin (Opisthocomus hoazin), an odd and enigmatic bird that defies classification.

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes –including river dynamics– which allow small populations to differentiate and disperse into secondary contact.

Disjunct, pantropical distributions are a common pattern among avian lineages, but disentangling multiple scenarios that can produce them requires accurate estimates of historical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re‐examining their phylogenetic relationships and divergence times with genome‐scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon genera with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well‐resolved hypothesis of relationships among trogon genera. Trogons comprise three clades, each confined to one of three biogeographical regions: Africa, Asia and the Neotropics, with the African clade sister to the others. These clades diverged rapidly during the Oligocene‐Miocene transition. Our biogeographical analyses identify a Eurasian origin for stem trogons and a crown clade arising from ancestors broadly distributed across Laurasia and Africa. The pantropical ranges of trogons are relicts of a broader Afro‐Laurasian distribution that was fragmented across Africa, Asia and the New World in near coincident fashion during the Oligocene‐Miocene transition by global cooling and changing habitats along the Beringian land bridge and North Africa.

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GC

Phylogenetic analyses of large-scale datasets sometimes fail to yield a satisfactory resolution of the relationships among taxa for a number of nodes in the tree of life. This has even been true for genome-scale datasets, where the failure to resolve relationships is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes in the tree of life, and taxon sampling, different analytical methods, and/or data-type effects are thought to further confound analyses. Observed conflicts among gene trees arise from both biological processes and artefactual sources of noise in analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigidae). We observed extensive conflict among genes for all data types and datasets even after we removed potentially problematic loci. Edge-based analyses increased congruence and examined the impact of data type, GC content variation (GCCV), and outlier genes on analyses. These factors had different impact on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the position of Hoatzin was highly variable, but we found that data type was correlated with the signals that support different placements of the Hoatzin. However, the resolution with the most support in our analyses was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding) per se, was correlated with an owl + Accipitriformes signal. Eliminating high GCCV loci increased the signal for an owl + mousebird relationship. Difficult edges (i.e., characterized by deep coalescence and high gene-tree estimation error) are hard to recover with all methods (including concatenation, multispecies coalescent, and edge-based analyses), whereas "easy" edges (e.g., flamingos + grebes) can be recovered without ambiguity. Thus, the nature of the edges, rather than the methods, is the limiting factor. Categorical edge-based analyses can reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant further examination in future phylogenomic studies. We suggest that edge-based analyses provide a tool that can increase our understanding about the parts of the avian tree that remain unclear, even with large-scale data. In fact, our results emphasize that the conflicts associated with edges that remain contentious in the bird tree may be even greater than appreciated based on previous studies.

Diversity does not drive speciation The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments relative to the tropics. Thus, for this group of birds, diversification in temperate to Arctic regions followed by the movement and retention of species in the tropics results in their higher local levels of species diversity. Science , this issue p. 1343 ; see also p. 1268

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., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Choco and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.

We identify key interdisciplinary questions and approaches to understanding the paleogeographic and biotic history of Amazonia. We discuss the importance of comparing evolutionary taxonomic units across groups and considering their particular environmental affinities as a framework for a mechanistic understanding of how the diversity of Amazonia was assembled across space and time. Although lineage diversity of the Amazonian biota is often quite old, current evidence indicates that much of Amazonia’s observed “species-level” diversity, as exemplified by birds, mammals, and butterflies, is young, mostly dating to the Quaternary. Much of the modern Amazonian landscape, including in particular its hydrological and environmental systems, was shaped over the Pliocene and Quaternary (last 5 Ma), yet significant landscape change affecting the evolution of biotas is less than 2 million years old.

Jacamar species occur throughout Amazonia, with most species occupying forested habitats. One species-complex, Galbula leucogastra/chalcothorax, is associated to white sand ecosystems (WSE). Previous studies of WSE bird species recovered shallow genetic structure in mtDNA coupled with signs of gene flow among WSE patches. Here, we characterize diversification of the G. leucogastra/chalcothorax species-complex with dense sampling across its distribution using mitochondrial and genomic (Ultraconserved Elements, UCEs) DNA sequences. We performed concatenated likelihood and Bayesian analysis, as well as a species-tree analysis using ∗BEAST, to establish the phylogenetic relationships among populations. The mtDNA results recovered at least six geographically-structured lineages, with G. chalcothorax embedded within lineages of G. leucogastra. In contrast, both concatenated and species-tree analyses of UCE data recovered G. chalcothorax as sister to all G. leucogastra lineages. We hypothesize that the mitochondrial genome of one of the G. leucogastra lineage (Madeira) was captured into G. chalcothorax in the past. We discuss how WSE evolution and the coevolution of mtDNA and nuclear genes might have played a role in this apparently rare event.

Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species’ ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized.

Aim: Understanding patterns of endemism is a key to deciphering the history of biotas and setting conservation priorities, but resolving the complexity of distributional patterns quantitatively into areas of endemism is often a difficult task. We report here an analysis of a comprehensive biodiversity dataset for the study of endemism, including virtually all vouchered records available for resident land birds of Mexico (> 100,000 georeferenced data points for all 780 species). Location: Mexico. Methods: The dataset was analysed with methods that recover areas without assuming prior endemic status for any species. This grid-based method for detecting areas of endemism considers co-occurrence and exclusiveness of species in alternative sets of geographic cells at different spatial resolutions, and finds optimal sets using heuristic, computationally intensive searches. Results: We provide the most detailed study of endemism in Mexico to date. Our analysis recovered 17 of 18 previously recognized areas of endemism for Mexican birds, plus many additional areas clearly supported by distributional data totalling 33 areas of endemism at different spatial scales. These areas cover 70% of the country's surface and form a network of nested and partially overlapping regions, some of which are also disjoint. Main conclusions: This picture contrasts strongly with previous conceptions of areas of endemism as non-overlapping and spatially simple in terms of scale. Our results reveal that endemism may be spatially complex and shed new light on its role as a key manifestation of biodiversity. Species identified as endemic to these areas comprise > 30% of the land birds of Mexico, with a disproportionately large fraction endangered according to IUCN or SEMARNAT. Fil: Bertelli, Sara Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina Fil: Szumik, Claudia Adriana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina Fil: Giannini, Norberto Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; Argentina Fil: Navarro Sigüenza, Adolfo G.. Universidad Nacional Autónoma de México; México Fil: Peterson, A. Townsend. University of Kansas; Estados Unidos Fil: Cracraft, Joel. American Museum Of Natural History; Estados Unidos

A revision of the avian Neotropical genus Automolus and the Furnariidae family points to the paraphyly of A. infuscatus and reveals a species complex comprising A. infuscatus, A. ochrolaemus, A. paraensis, A. leucophthalmus, A. lammi and A. subulatus, the latter historically classified in the genus Hyloctistes. Detailed knowledge of the taxonomy, geographic distribution, phylogenetic relationship and divergence times of a taxon allows exploration of its evolutionary history and the testing of different scenarios of diversification. In this context, we studied the A. infuscatus complex using molecular data in order to unveil its cryptic diversity and reveal its evolutionary history. For that we sequenced two mitochondrial (ND2 and cytb) and three nuclear markers (G3PDH, ACO, Fib7) for 302 individuals belonging to all species in the complex and most described subspecies. Our analysis supports the paraphyly of A. infuscatus, indicating the existence of at least two distinct clades not closely related. The remaining species were all recovered as monophyletic. Notwithstanding, a well-structured intraspecific diversity was found with 19 lineages suggesting substantial cryptic diversity within the described species. A. subulatus was recovered within the complex, corroborating its position inside the genus. In spite of the high congruence between distributions of different lineages, with several sister lineages currently separated by the same barriers, the temporal incongruence between divergences over the same barriers reveals a complex evolutionary history. While older events might be related to the emergence of barriers such as the Andes and major Amazonian rivers, younger events suggest dispersal after the consolidation of those barriers. Our analysis suggests that the complex had its origin around 6 million years (Ma) and inhabited Western Amazonia in Late Miocene-Early Pliocene. Considering the riparian habit of species in its sister clade, the rise and early diversifications of the complex may be related to the establishment of terra firme forests as it changed from a floodplain to a fluvial system. The late Amazonian colonization by A. subulatus and A. ochrolaemus lineages may have been hampered by the previous existence of well established A. infuscatus lineages in the region. © 2016 Elsevier Inc.

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10&times, ) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

Relationships among Neoaves, a group comprising approximately 95% of all extant birds, are difficult to resolve because of multiple short internodes presumably created by a rapid evolutionary radiation around the K/Pg boundary. This difficulty has plagued both morphological and molecular studies. Compared with molecular studies with extensive taxon and character sampling, morphological datasets have largely failed to provide insight into the phenotypic evolutionary transitions of the neoavian radiation. Extinct neoavian taxa remain an understudied but critical key to resolving relationships among these problematic stem lineages and understanding evolutionary changes in structure and function. Adzebills (Aptornis), some of the most phylogenetically controversial fossil neoavians, are extinct terrestrial birds endemic to New Zealand since at least the early Miocene. Past morphological studies have placed adzebills as a sister taxon to the flightless Kagu of New Caledonia (Rhynochetos jubatus) or to the land- and waterfowl group Galloanseres. Recent molecular studies reveal the Kagu and Sunbittern (Eurypyga helias) to be sister taxa, whereas adzebills have been postulated to be within Rallidae (rails, gallinules, and coots) or the sister taxon of Sarothruridae (flufftails) or Ralloidea (finfoots, flufftails, and rails). To better resolve the position of adzebills and begin constructing a fine-scale total evidence phylogenetic dataset for the base of Neoaves, we constructed a new and more comprehensive morphological dataset of 368 discrete osteological characters for 38 extant and two extinct taxa that includes extensive sampling of nearly all neoavian stem lineages. We then combined this dataset with 32 DNA sequences of the slowly evolving nuclear RAG1 and RAG2 genes. Morphological results place adzebills as the sister taxon of trumpeters (Psophia) within core Gruiformes and confirm strong support for a Kagu+Sunbittern sister group (99% bootstrap value). Results for analyses of the combined data were identical, and the adzebill+trumpeter clade was supported by a 99% Bayesian clade credibility value. Although the Kagu+Sunbittern sister group is consistent with recent molecular hypotheses, the adzebill+trumpeter group is novel.

Reconstructing relationships among extant birds (Neornithes) has been one of the most difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains (at least partially) unresolved. Thus far, the most difficult problem is the relationship among the orders of Neoaves, the major clade that includes the most (~95%) named bird species. This clade appears to have undergone a rapid radiation near the end Cretaceous mass extinction (the K-Pg boundary). On the other hand, if one embraces a “glass half full” view, the fact that most orders in Neoaves can be placed into seven clades, recently designated the “magnificent seven,” could be viewed as remarkable progress. We propose that the dawning era of whole-genome phylogenetics will only resolve the remaining relationships, if we improve data quality, exploit information from other sources (i.e., rare genomic changes), and learn more about the functional and evolutionary landscape of avian genomes. Of course, it is possible that the remaining unresolved relationships are unresolvable regardless of the data available, but we suggest that the community should avoid this conclusion until more data collection has been completed and improved analyses have been conducted. We say this because there is ample evidence that estimates of avian phylogeny based on large-scale datasets may be affected by well-characterized artifacts (e.g., long-branch attraction, heterotachy, and discordance among gene trees) and by subtle “data-type effects” that reflect poor fit to empirical data for available models of sequence evolution. Even if these analytical challenges can be addressed, we need to integrate phylogenomic and fossil data. Finally, we also emphasize that, regardless of the resolution (or lack thereof) for relationships among major avian clades, we are only at the dawn of the phylogenomics of birds. Large-scale molecular data remain unavailable for the vast majority of the ~10,000 named bird species, and those named bird species probably represent an underestimate of the true number of distinct evolutionary lineages of birds (whether or not those lineages are assigned the rank of species) by as much as threefold. A true biodiversity genomics effort in birds is likely to reveal many additional examples of cases where it is very difficult to resolve relationships; the effort to resolve as many of those relationships as possible will represent a major scientific achievement and provide lessons for phylogenomic studies in other parts of the tree of life.

Significance Our understanding of the factors that affected the diversification of passerines, the most diverse and widespread bird order (Passeriformes), is limited. Here, we reconstruct passerine evolutionary history and produce the most comprehensive time-calibrated phylogenetic hypothesis of the group using extensive sampling of the genome, complete sampling of all passerine families, and a number of vetted fossil calibration points. Our phylogenetic results refine our knowledge of passerine diversity and yield divergence dates that are consistent with the fossil record, and our macroevolutionary analyses suggest that singular events in Earth history, such as increases in Cenozoic global temperature or the colonization of new continents, were not the primary forces driving passerine 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.

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Mixed carbonate-siliciclastic platforms developed in the onshore and offshore zones of several basins along the Amazonian coast starting in the Palaeocene. The shutdown of Miocene carbonate accumulation in distinct tectonic settings shows different evolutionary histories along the Eastern Amazonian coast. The shutdown has been attributed to the abundant siliciclastic fluvial inflow from the Andean Amazon River during the late Miocene. The combination of previously collected geological information and new stratigraphic data from the Oligocene-Miocene transgressive-regressive Pirabas-Barreiras sequence exposed on the Bragantina Platform of the Eastern Amazonian coast reveals the collapse of the carbonate platform by the Barreiras fan delta deposits during the middle Miocene. The development of the Barreiras fan delta, fed by a cratonic source exposed during the Langhian (15–10 Ma) sea-level fall, was concomitant with the so-called Cratonic Amazon River that preceded the transcontinental Andean Amazon River. The climax of sea-level fall caused the maximum expansion of the Barreiras fan delta, which reached the Marajo and Para-Maranhao basins. The progressive denudation of the region, low fluvial inflow, and extensive Tortonian sea-level fall (11–8 Ma) resulted in the inactivity of the Barreiras Delta. Consequently, the exposure and subsequent intense lateritization of these degraded deposits generated an extensive unconformity that lasted until the deposition of Pleistocene Post-Barreiras sediments.

Aim We develop a conceptual framework for integrating evolutionary history and ecological processes into studies of biotic assembly. Location Global. Methods We use theoretical and empirical examples to demonstrate that species distributions are non-random outcomes of first-order processes of biotic evolution: allopatry (isolation of populations), speciation and dispersion of biotas across landscapes. We then outline generalizable steps for integrating methods of phylogenetic and historical biogeographical analyses into studies of biotic assembly. Results We present a framework that can be applied to any biotic assemblage amenable to phylogenetic and historical biogeographical analyses, can accommodate changes in spatial extent and temporal scale, and will facilitate comparison of assembly processes across biotas. Additionally, we demonstrate the utility of an historical approach for providing context to ecological influences on evolutionary processes, such as trait evolution. Main conclusions By focusing on reconstructing the histories of individual lineages, an historical approach to assembly analysis can reveal the timing and underlying processes guiding biotic assembly, making it possible to disentangle the roles of history and ecology in the assembly process.

International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

We present a new molecular phylogeny of the three main radiations of nightjars (Caprimulgidae), restricted to the New World. Both mitochondrial and nuclear markers were sampled, and ancient DNA from museum skin specimens was an important source of sequence data for many taxa. Intraspecific diversity is high in the nightjars, with many traditionally defined species further divided into subspecies. By dense sampling at the species and subspecies level, we were able to investigate the molecular diversity among the majority of recognized subspecies. This resulted in the identification of new phylogenetic species in addition to finding molecular support for recent taxonomic modifications such as the division of the Whip-poor-will (Antrostomus vociferus Wilson, 1812) into two species. Other species that we suggest should be split into two or more phylogenetic species include Caprimulgus longirostris Bonaparte, 1825, Chordeiles acutipennis (Hermann, 1783), Nyctidromus albicollis (Gmelin, 1789), and Nyctiprogne leucopyga (Spix, 1825). We also propose substantial modifications to the generic structure within the family, with some genera being enlarged (including Hydropsalis, Nyctidromus, and Nyctiprogne), whereas others are discontinued (including Eleothreptus and Uropsalis). All New World species of Caprimulgus are moved into other genera. The resulting phylogeny provides the most up-to-date and complete taxonomic review for the New World diversity of the family. © 2014 The Linnean Society of London

Dendrocincla woodcreepers are ant-following birds widespread throughout tropical America. Species in the genus are widely distributed and show little phenotypic variation. Notwithstanding, several subspecies have been described, but the validity of some of these taxa and the boundaries among them have been discussed for decades. Recent genetic evidence based on limited sampling has pointed to the paraphyly of D. fuliginosa, showing that its subspecies constitute a complex that also includes D. anabatina and D. turdina. In this study we sequenced nuclear and mitochondrial markers for over two hundred individuals belonging to the D. fuliginosa complex to recover phylogenetic relationships, describe intraspecific genetic diversity and provide historical biogeographic scenarios of diversification. Our results corroborate the paraphyly of D. fuliginosa, with D. turdina and D. anabatina nested within its recognized subspecies. Recovered genetic lineages roughly match the distributions of described subspecies and congruence among phylogenetic structure, phenotypic diagnosis and distribution limits were used to discuss current systematics and taxonomy within the complex, with special attention to Northern South America. Our data suggest the origin of the complex in western Amazonia, associated with the establishment of upland forests in the area during the early Pliocene. Paleoclimatic cycles and river rearrangements during the Pleistocene could have, at different times, both facilitated dispersal across large Amazonian rivers and the Andes and isolated populations, likely playing an important role in differentiation of extant species. Previously described hybridization in the headwaters of the Tapajós river represents a secondary contact of non-sister lineages that cannot be used to test the role of the river as primary source of diversification. Based on comparisons of D. fuliginosa with closely related understory upland forest taxa, we suggest that differential habitat use could influence diversification processes in a historically changing landscape, and should be considered for proposing general mechanisms of diversification.

Amazonia is a ‘source’ of biodiversity for other Neotropical ecosystems, but which conditions triggerin situspeciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.

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Quintero, E., Ribas, C. C. & Cracraft, J. (2012). The Andean Hapalopsittaca parrots (Psittacidae, Aves): an example of montane-tropical lowland vicariance. —Zoologica Scripta, 42, 28–43. We describe a phylogenetic and biogeographical pattern connecting high montane biotas to those of the lowlands, as exemplified by the exclusively montane parrot genus Hapalopsittaca and its lowland sister genus Pyrilia, both nested within Tavares et al.’s “amazons and allies” clade. As Hapalopsittaca is the only genus within the “amazons and allies” clade that is exclusively distributed in the Andes, the optimization leads to the inference that the ancestral distribution of the branch leading to Pyrilia + Hapalopsittaca was lowland. Museum specimens were examined to determine basal diagnosably distinct taxonomic units. Based on this analysis, mitochondrial sequences (cyt b and ND2 genes) from 17 individuals, mostly from toe pads, and representing all basal taxa within Hapalopsittaca, were obtained. A divergence-dating analysis using both nuclear (RAG-1) and mitochondrial (cyt b) genes was conducted to explore whether the uplift of the Andes coincides temporarily with the origin of this montane group, and thus might be causally linked to its origin. Molecular dating estimates the split between Hapalopsittaca and Pyrilia to have occurred between 6.6 and 8.0 Myr; thus, the timing of this highland/lowland disjunction is consistent with that of the final uplift of the Central Andes, supporting a hypothesis of vicariance due to Andean uplift. These results suggest that the taxonomic assembly of montane biotas may be, at least in part, explained by events of Earth history rather than by long-distance dispersal and colonization. Diversification within Hapalopsittaca and the origin of current species are more recent in time and probably are related to Pleistocene climatic oscillations, as has been shown in other montane groups.

Many hypotheses have been proposed to explain high species diversity in Amazonia, but few generalizations have emerged. In part, this has arisen from the scarcity of rigorous tests for mechanisms promoting speciation, and from major uncertainties about palaeogeographic events and their spatial and temporal associations with diversification. Here, we investigate the environmental history of Amazonia using a phylogenetic and biogeographic analysis of trumpeters (Aves: Psophia ), which are represented by species in each of the vertebrate areas of endemism. Their relationships reveal an unforeseen ‘complete’ time-slice of Amazonian diversification over the past 3.0 Myr. We employ this temporally calibrated phylogeny to test competing palaeogeographic hypotheses. Our results are consistent with the establishment of the current Amazonian drainage system at approximately 3.0–2.0 Ma and predict the temporal pattern of major river formation over Plio-Pleistocene times. We propose a palaeobiogeographic model for the last 3.0 Myr of Amazonian history that has implications for understanding patterns of endemism, the temporal history of Amazonian diversification and mechanisms promoting speciation. The history of Psophia , in combination with new geological evidence, provides the strongest direct evidence supporting a role for river dynamics in Amazonian diversification, and the absence of such a role for glacial climate cycles and refugia.

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents.

Genetic elements determine phenotypes of organisms by interacting with environments. Despite genetic diversity within and between species being the fundamental basis of biological diversity, its contribution has been long neglected in biodiversity studies. This situation is rapidly changing as quantification of genetic diversity, from intraspecific up to the ecosystem level, has become more accessible owing to the development of next-generation sequencing technologies (NGSTs). Whole-genome sequencing techniques provide two specific approaches for accessing genetic diversity at large scales: metagenomics (environmental genomics) and EST (Expressed Sequence Tag) comparisons. The former has been applied successfully in the profiling of different microbial biomes, and it is particularly interesting in understanding their ecosystem structure and function. The latter is particularly useful in the studies of adaptation and the assessment of functional traits. Unquestionably, advances in the genomic sciences combined with a new generation of ecological and evolutionary science will boost new approaches to global and local assessments of biodiversity changes, and more importantly, will surely reframe the questions we are asking in biodiversity science.

Phylogenetic relationships among the Tyrannides were assessed using over 4000 base pairs of nuclear recombination activating 1 (RAG-1) and 2 (RAG-2) DNA sequence data from about 93% of all described genera, which represents the most complete assessment of relationships for this diverse New World radiation to date. With this sampling we propose a significantly expanded interpretation of higher-level relationships within the group. The Tyrannides are shown to be comprised of six major lineages, all of which represent traditional family-level taxa (sensuFitzpatrick, 2004a and Snow, 2004a,b; del Hoyo et al., 2004): (i) manakins (Pipridae); (ii) cotingas (Cotingidae); (iii) the sharpbill (Oxyruncus) + onychorhynchine flycatchers (Onychorhynchini); (iv) tityrines (Tityridae); (v) rhynchocycline flycatchers (Rhynchocyclidae); and (vi) the tyrant flycatchers (Tyrannidae). In addition, the RAG data recovered isolated lineages with uncertain relationships, including Neopipo, Platyrinchus, Piprites, and Tachuris. The Pipridae are the sister-group to all the other Tyrannides. Within the latter, the clade ((Oxyruncidae + Tityridae) + Cotingidae) is the sister-group of the Tyrannoidea. Within the Tyrannoidea, the Rhynchocyclidae and their allies are sisters to Neopipo + Tyrannidae. Using our phylogenetic hypothesis, we propose the first comprehensive phylogenetic classification that attempts to achieve isometry between the tree and a classification scheme using subordination and phyletic sequencing. This study thus provides a phylogenetic framework for understanding the evolution of this diverse New World assemblage, and identifies many avenues for further systematic study. © The Willi Hennig Society 2009.

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well-supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time-frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods.

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Early stages of avian evolution in the Southern Hemisphere remain largely unsampled. Here, we describe an avian fossil from near the Cretaceous-Tertiary (K-T) boundary representing one of the oldest records of birds on New Zealand. The specimen comprises a tarsometatarsus diagnosable to the level of Or nithurae by two derived features: presence of a globose inter cotylar eminence and presence of two proximal vascular fo ramina. The fossil was collected from a section cut by the Wai makariri River near Otarama Railway Station on the South Island of New Zealand (Figure 1). Morphological similarities shared with waterbirds such as Procellariiformes, Gaviiformes, and Rallidae suggest an aquatic ecology for the Waimakariri bird, but do not provide evidence for placement in any extant clade. Although fragmentary, this fossil demonstrates that birds other than penguins reached New Zealand by at latest the ear liest Paleocene. New Zealand is well known for a rich subfossil avifauna in cluding the recently extinct moa (Dinornithiformes), flightless songbirds (acanthisittid wrens: e.g., Pachyplichas yaldwyni, Dendroscansor decurvirostris), and the giant raptor Harpagornis

SUMMARY A new fossil genus and species, Onychopteryx simpsoni, is described for a proximal end of a tarsometatarsus from the lower Eocene (Casamayor Formation) of Argentina. Onychopteryx is considered most closely related to the Opisthocomidae but is sufficiently distinct to be placed in its own family, the Onychopterygidae. Onychopteryx indicates that the Opisthocomiformes had differentiated by the early Eocene and were present in South America at that time.

Of the myriad birds with uncertain phylogenetic aYnities and convoluted taxonomic histories, perhaps none rivals the Bornean Bristlehead (Pityriasis gymnocephala) for the sheer number of families to which it has been allied and the resulting confusion as to its biogeographic history. The sole member of the genus is endemic to Borneo, where it is an uncommon resident of lowland and hill forests (Colenutt, 2002; Sheldon et al., 2001). It is seldom seen in the Weld, and long absences from suitable habitat punctuated by brief appearances of vociferous Xocks suggest that the species is highly nomadic (Witt and Sheldon, 1994). It is a relatively large passerine with a heavy, hooked bill. The plumage is mostly black, but with red and yellow feathers around the head and thighs. Plumage of the neck and head is coarse and stiV, giving rise to the English name, and it has been of particular interest to feather anatomists because of its unusual structure (Prum and Brush, 2002). The Bristlehead’s odd appearance and uncertain relationships led Mayr and Amadon (1951) to describe it as “one of the strangest members of all the Oscines.” Ahlquist et al. (1984) provided a thorough chronology of the various taxonomic assignations for Pityriasis, which we brieXy recount. Early taxonomic treatments placed Pityriasis closest to the genera Cracticus and Gymnorhina (Gadow, 1883; Temminck, 1835), similarly sized and heavy-mandibled genera from Australia and New Guinea. The Wrst dissenting view arose by the end of that century when Shelford (1899) suggested that it had aYnities to Eulabes (DGracula) and thus was a starling (Sturnidae). Confusion

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short-tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Choco ´ , Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.