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The crustacean family Ampithoidae is one of the most abundant invertebrate families associated with macroalgae in shallow marine waters. Ampithoe, the largest genus, was previously documented as non‐monophyletic by phylogenetic analyses based on morphological and molecular characters. Here, we reconstructed a multi‐gene phylogeny of Ampithoidae with the first data of the southwestern Atlantic Ocean. We performed the first biogeographic analyses for the family, which indicated its origin in the Indo‐West Pacific, with subsequent dispersion to the Atlantic Ocean around the Eocene. Divergence times suggest that the diversification of Ampithoidae is congruent with the brown algae crown radiation, which allowed the colonization of new environments. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions Several lines of evidence have noted that open vegetation biomes in the Neotropics are younger than moist forests, leading us to question which historical processes shaped the current species distribution patterns in these new biome formations. Here we investigate the temporal patterns of speciation and colonisation from surrounding biomes (Amazonia, Atlantic Forest and Cerrado) in the Caatinga historical assembly of squamate species, to understand the role of geomorphological events and climate change in driving its diversification.Neotropics.Squamata (snakes, lizards and amphisbaenians).We used a phylogenetic tree and occurrence data for 459 squamate species distributed throughout four different biomes (Amazonia, Atlantic Forest, Cerrado and Caatinga) to reconstruct ancestral geographic ranges using the R package BioGeoBEARS. We used BAMM to estimate the rates of species diversification.Our results indicate that the current diversity patterns of squamates in the Caatinga were a result of pervasive faunal exchanges from adjacent biomes since the Paleogene, with similar numbers of dispersal events in each source area. The Neogene period was determinant in the diversification process, leading to the current assembly patterns of this group in the Caatinga.The landscape transformation and climate change that increased aridity in northeastern Brazil probably shaped the diversification of dry‐adapted squamates in the Caatinga, like tropidurid lizards. However, the Pleistocene climatic fluctuations associated with the highly heterogeneous gradients of topography, geology, soils, climatic conditions, and different vegetation physiognomies could have facilitated faunal exchange with their neighbouring forested biomes, explaining the current presence of some typical forested lineages inside the Caatinga domain and help us to clarify the current distribution patterns of squamates in this region. [ABSTRACT FROM AUTHOR]

Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages. [ABSTRACT FROM AUTHOR]

ABSTRACT Mechanisms driving the spatial and temporal patterns of species distribution in the Earth's largest habitat, the deep ocean, remain largely enigmatic. The late Miocene to the Pliocene (~23–2.58 Ma) is a period that was marked by significant geological, climatic, and oceanographic changes. This transitional period spurred widespread species diversification, particularly among widely distributed benthic scavengers, such as amphipods. Here, we take step toward understanding the long‐term evolutionary processes of amphipod colonization and diversification in the deep ocean by focusing on the model genus Eurythenes S. I. Smith in Scudder, 1882. These large‐bodied scavengers play key roles in benthic communities. We constructed a time‐calibrated phylogeny using two mitochondrial DNA genes by analyzing publicly available data on 14 species of Eurythenes across a global depth range from 839 to 8081 m. The resulting phylogenetic tree reveals a diverse clade, with a common ancestor originating around 11.81 Ma. A gradual increase in the effective population size of Eurythenes was observed, particularly during the Pliocene (~4 Ma). The net diversification rate remained almost constant, with slight increases between the Miocene and Pliocene (~8–4 Ma), and most new species appeared during the latter period. Additionally, reconstruction of the ancestral area suggested that the common ancestor of Eurythenes had a global distribution. A combination of dispersal and sympatric processes, along with environmental factors, such as changes in ocean temperature and sea level, contributed to the present biogeographic distribution of these species. Our findings highlight the importance of historical events, such as plate tectonics and changes in deep‐water circulation, in driving the rapid speciation of Eurythenes and underscore their essential role in shaping deep‐ocean biodiversity.

Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity. [ABSTRACT FROM AUTHOR]

Fruit flies (Tephritidae: Dacini) are a frugivorous insect group that exhibit high endemic diversity in the rainforests of Australia and the western Pacific. In this region, biogeography has been influenced by tectonic plate movements and cycles of isolation and re‐connection of landmasses and rainforest habitats during glacial periods. However, how such factors have influenced the speciation and historical dispersal of the regional Dacini is largely unknown. To address this, we use a dated phylogeny to reconstruct the biogeographical history of the tribe. We found the Dacini radiated eastward into the Pacific islands largely from sources in New Guinea. We also found evidence for historical dispersal from both Australia and New Guinea into New Caledonia, a pathway unique to this island compared with neighbouring islands. There was also evidence for multiple, bidirectional dispersal events between Papua New Guinea and Australia, likely facilitated by the cyclically exposed Torres Strait land bridge. Cape York in far northern Australia was likely the only entry point for species dispersing into Australia; there was no evidence for entry of flies into Australia directly from West Papua or Wallacea. Several lineages radiated after entering Australia, such as members of the Bactrocera dorsalis species group. Within Australia, speciation was not associated with the biogeographic barriers known to have impacted other rainforest fauna in eastern Australia. Overall, we demonstrate that isolation between islands and large landmasses is important in the evolution of the Australo‐Pacific Dacini, but the reason for their extensive radiation within Australia and Papua New Guinea remains unclear. [ABSTRACT FROM AUTHOR]

Aim: Shifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic‐based analyses, to explore how changes in temperature and increasing aridity during the Neogene influenced the diversification of the Australian blindsnakes. We tested whether diversification rates differ between arid‐adapted and mesic‐adapted lineages. Taxon: Typhlopidae, Anilios blindsnakes. Location: Australia. Materials and Methods: We estimated the historical biogeography of blindsnakes using BioGeoBEARS. We synthesised multiple approaches to reconstruct paleotemperature and paleoaridity of Australia during the Neogene. We fitted several birth‐death models and estimated diversification rates under paleoenvironmental conditions using RPANDA. We further compared diversification rates between arid‐adapted lineages versus mesic‐adapted lineages using ClaDS and GeoHiSSE. Results: Ancestral area estimation indicated Australian blindsnakes have tropical grassland origins. We found that Australia‐specific regional paleotemperature and paleoaridity provided a better explanation for diversification rate variation than global paleotemperature. Specifically, our best‐fitting model indicated that speciation rates of blindsnakes decreased with increasing aridity. We found no difference in diversification rates between arid‐ and mesic‐adapted lineages. Main Conclusions: Soon after dispersing to Australia, the common ancestors of Australian blindsnakes diversified rapidly in mesic habitats during the early Miocene. However, as the continent became increasingly arid, diversification rates decreased. We found that shifts in the environment led to the emergence of two major clades: one remaining in primarily mesic habitats and the other adapting to the expanding arid biome. Our results emphasise the importance of both arid and tropical biomes as sources and sinks of diversification. [ABSTRACT FROM AUTHOR]

Aim: Although New Caledonia (NC) is now considered an oceanic island that emerged ca. 60 Ma, a few terrestrial clades are significantly older, raising the question of the origin of these groups. Classically, old lineages on more recent islands are hypothesized to originate through a process of hopping on now‐vanished islands (i.e., island‐hopping hypothesis) or other territories. We aim to test this hypothesis by studying a group of cockroaches with several lineages found in NC. Location: New Caledonia, New Zealand, Australia. Taxon: Insects: Blattodea. Methods: We generated a dated phylogeny for blattid cockroaches (Blattidae and Tryonicidae) using Bayesian inference along with fossil calibrations. We reviewed studies on the palaeogeography of the Southwest Pacific region, including hypotheses about the existence of yet‐to‐be‐discovered past islands, and constructed biogeographical tests accordingly. We computed ancestral area estimation under different models in BioGeoBEARS (DEC, BAYAREALIKE, DIVALIKE, with or without +J) to test the role of an island‐hopping hypothesis in the establishment of NC blattid fauna. Results: We find divergence times older than 60 Ma for two NC clades. We show that these 'old' endemic lineages can partially be explained by indirect dispersal from Australia or New Zealand through now disappeared islands. Alternative hypotheses suggest multiple independent colonizations of NC from Antarctica or Australia. Main Conclusions: Our results indicate that island‐hopping may explain the presence of old groups in NC. The island‐hopping hypothesis is nonetheless only supported for a period‐area from which geological evidence is ambiguous. Our work highlights both the fruitful interactions between geology and biogeography and the underlying difficulties. The multiple colonization events inferred for NC provide additional insights into the composite nature of NC biota. [ABSTRACT FROM AUTHOR]

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

During the radiation of a clade, diversification rates can show temporal patterns such as a speedup or slowdown, which might relate to different ecological and evolutionary mechanisms. The temporal dynamics of diversification of whole clades are often visualised as a lineage-through-time (LTT) plot, which traces the number of reconstructed lineages at different time points. However, clades do not radiate evenly across space and may show different temporal dynamics in different regions. As such, a biogeographic approach is required to more completely understand temporal diversification dynamics. Here, I present a tool to extract temporal diversity information across different biogeographic regions from the output of commonly used ancestral range estimation models implemented in the R package BioGeoBEARS. The lineages through space and time (LTST) plot allows for visualisation of diversification dynamics in different regions, formatted in an accessible way which can be used for further quantitative analysis.

Anuran amphibians have intensively been studied to understand Amazonian biodiversity. Improved methods and sampling has revealed that many widespread nominal species in fact are complexes of species with smaller allopatric ranges. Pan-Amazonian anuran species are rather an exception. In a case study using the three-striped poison frog (Anura: Dendrobatidae: Ameerega trivittata), we ask how the pan-Amazonian distribution of this taxon can be explained and hypothesize that dispersal has played a major role. Species delimitation and intraspecific relationships of the study species were examined from novel and existing (GenBank) sequences of the mitochondrial 16S rRNA gene from 108 specimens of 38 localities using maximum likelihood and Bayesian methods. We performed BioGeoBEARS models using a time-calibrated population tree to reconstruct the biogeographic history. Our results support that A. trivittata is a pan-Amazonian species scattered over its geographic range. Being of Late Miocene origin, the species rapidly spread into newly available space and repeatedly dispersed for-and backward, while vicariance played a major role only in the Early Pliocene. We suggest that intrinsic morphological and life history characteristics (adult size, relative reproductive success) make A. trivittata a more successful disperser than other species, so that riverine barriers are more permeable and hamper allopatric speciation. We conclude that there is no universal causality explaining Amazonia biodiversity, because species-specific biological characteristics are key determents of biogeographical histories. Comparatively better dispersal advantages foster larger geographic ranges and can explain pan-Amazonian distributions. [ABSTRACT FROM AUTHOR]

Nemognathinae is the most widespread subfamily of Meloidae, with ~600 species, and includes the only blister beetles distributed in Australia and on islands of the western Pacific. Four tribes are recognised based on morphology: Stenoderini, Palaestrini, Horiini and Nemognathini. Using two mitochondrial (16S , COI) and three nuclear markers (CAD , 28S , ITS2), and both maximum likelihood and Bayesian approaches, this study describes the evolutionary history of Nemognathinae based on molecular data for the first time. We provided a fossil-calibrated phylogeny that unravels the phylogenetic relationships among the tribes and among most of the genera, and a reconstruction of the biogeographic history using a parametric approach. Our results recognised the four tribes that were described previously based on morphology and revealed the presence of another well-differentiated clade corresponding to the genus Zoltanzonitis. Phylogenetic relationships among the tribes are well supported, with Stenoderini as the most ancient lineage, followed by Zoltanzonitini, Palaestrini, Horiini and Nemognathini. A few long-standing genera within Nemognathini (Nemognatha , Zonitis , Stenoria) and the nominate subgenus Stenodera (Stenodera) were recovered as polyphyletic. In addition, biogeographic analyses revealed the origin of the subfamily in the Old World during the Eocene, and the associated diversification into the five tribes astride the Eocene and Oligocene between 46 and 30 Ma. Based on these results we propose the new tribe Zoltanzonitini, and the elevation of the subgenus Pronemognatha to genus level, new status. In addition, Zonitoschema breveapicalis new comb. , Z. curticeps new comb. and Z. pulchella new status are proposed. ZooBank: urn:lsid:zoobank.org:pub:72EECC6D-36A6-4DD7-B4DB-D0692034E775. Nemognathinae is the most widespread Meloidae subfamily, with ~600 species, among which are the only blister beetle species that occur in Oceania. A comprehensive molecular phylogeny for the group is lacking. We investigated the history of this subfamily with a fossil-calibrated molecular approach, revealing the presence of a new tribe, the polyphyly of a few genera and an Eocene origin in the Old World. This work represents the first molecular phylogeny of Nemognathinae and contributes to revealing the evolutionary history of the Meloidae. [ABSTRACT FROM AUTHOR]

Dinosaurs dominated Mesozoic terrestrial ecosystems for ∼160 million years, but their biogeographic origin remains poorly understood. The earliest unequivocal dinosaur fossils appear in the Carnian (∼230 Ma) of southern South America and Africa, leading most authors to propose southwestern Gondwana as the likely center of origin. However, the high taxonomic and morphological diversity of these earliest assemblages suggests a more ancient evolutionary history that is currently unsampled. Phylogenetic uncertainty at the base of Dinosauria, combined with the subsequent appearance of dinosaurs throughout Laurasia in their early evolutionary history, further complicates this picture. Here, we estimate the distribution of early dinosaurs and their archosaurian relatives under a phylogenetic maximum likelihood framework, testing alternative topological arrangements and incorporating potential abiotic barriers to dispersal into our biogeographic models. For the first time, we include spatiotemporal sampling heterogeneity in these models, which frequently supports a low-latitude Gondwanan origin for dinosaurs. These results are best supported when silesaurids are constrained as early-diverging ornithischians, which is likely because this topology accounts for the otherwise substantial ornithischian ghost lineage, explaining the group's absence from the fossil record prior to the Early Jurassic. Our results suggest that the archosaur radiation also took place within low-latitude Gondwana following the end-Permian extinction before lineages dispersed across Pangaea into ecologically and climatically distinct provinces during the Late Triassic. Mesozoic terrestrial vertebrates are under-sampled at low paleolatitudes, and our findings suggest that heterogeneous sampling has hitherto obscured the true paleobiogeographic origin of dinosaurs and their kin., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Some plant lineages remain within the same biome over time (biome conservatism), whereas others seem to adapt more easily to new biomes. The c. 398 species (14 genera) of subfamily Cercidoideae (Leguminosae or Fabaceae) are found in many biomes around the world, particularly in the tropical regions of South America, Asia and Africa, and display a variety of growth forms (small trees, shrubs, lianas and herbaceous perennials). Species distribution maps derived from cleaned occurrence records were compiled and compared with existing biome maps and with the literature to assign species to biomes. Rainforest (144 species), succulent (44 species), savanna (36 species), and temperate (10 species) biomes were found to be important in describing the global distribution of Cercidoideae, with many species occurring in more than one biome. Two phylogenetically isolated species-poor temperate ( Cercis ) and succulent ( Adenolobus ) biome lineages are sister to two broadly distributed species-rich tropical clades. Ancestral state reconstructions on a time-calibrated phylogeny suggest biome shifts occurred throughout the evolutionary history of the subfamily, with shifts between the succulent and rainforest biomes, from the rainforest to savanna, from the succulent to savanna biome, and one early occurring shift into (or from) the temperate biome. Of the 26 inferred shifts in biome, three are closely associated with a shift from the ancestral tree/shrub growth form to a liana or herbaceous perennial habit. Only three of the 13 inferred transcontinental dispersal events are associated with biome shifts. Overall, we find that biome shifts tend to occur within the same continent and that dispersals to new continents tend to occur within the same biome, but that nonetheless the biome-conserved and biogeographically structured Cercidoideae have been able to adapt to different environments through time., Supplementary Information: The online version contains supplementary material available at 10.1007/s40415-024-01058-z., Competing Interests: Conflict of interestThe authors declare no financial or non-financial interests that are directly or indirectly related to the work submitted for publication., (© The Author(s) 2024.)

Aim: In the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero. Location: Global applications, with an example from the Americas. Taxon: All taxa, with an example from hummingbirds (Amazilia). Methods: Methods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a user‐friendly platform, which we term LEMAD (Lineage Extinction Model of Ancestral Distribution) that generalizes the likelihood described in GeoSSE for any number of areas and under several sets of geographic assumptions. We compare LEMAD and extinction‐free approaches using extensive simulations under different macroevolutionary scenarios. We apply our method to revisit the historical biogeography of Amazilia hummingbirds. Results: We find that accounting for the lineages removed from a tree by extinction improves reconstructions of ancestral distributions, especially when rates of vicariant speciation are higher than rates of in situ speciation, and when rates of extinction and range evolution are high. Rates of in situ and vicariant speciation are accurately estimated by LEMAD in all scenarios. North America as the most likely region for the common ancestor of hummingbirds. Main conclusions: Methods that neglect lineage extinction are less likely to accurately reconstruct true biogeographic histories of extant clades. Our findings on an empirical dataset reconcile the Eurasian origin of Amazilia with biogeographic reconstructions when lineage extinction is considered. [ABSTRACT FROM AUTHOR]

Fouquieriaceae consists of a single genus Fouquieria with eleven species occurring in arid and semiarid regions in Mexico and the southwestern USA. A recently developed phylogeny based on chloroplast DNA sequences provided strong support for the monophyly of the genus and the evolutionary species relationships. However, details of its evolutionary history remain unclear. Due to this uncertainty, additional information such as the evolution on its growth habit, reconstruction of the ancestral habitat, and on chromosome evolution is needed for a clear understanding of its evolutionary history. Different hypotheses concerning the shift of growth habits (succulent or woody) and the occupation of the ancestral habitat, and the chromosomal evolution in the family were analyzed. We assessed the ancestral distribution by fitting different biogeographic models. Our results suggest that Fouquieriaceae may have originated in two regions at the margins of the present geographic distribution of the genus: the Sonoran Desert and desert areas south of the Mexican Transvolcanic Belt. However, our results suggest that the ancestral lineage of Foquieriaceae was originated in desert habitats in central–southern Mexico with a basal chromosome number of n = 12, and a succulent habit, all of which may have allowed the dispersion of polyploid species to newly developed dry environments during the Late Miocene. [ABSTRACT FROM AUTHOR]

Aim: Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS, which implements several models in a common framework, allowing models to be compared with standard likelihood‐based methods of statistical model comparison. Ree and Sanmartín (Journal of Biogeography, 45, 741–749, 2018) critiqued the comparison of Dispersal–Extinction–Cladogenesis (DEC) and a modification of it, DEC+J, which adds the process of jump dispersal at speciation. DEC+J provides highly significant improvements in model fit on most (although not all) datasets. They claim that the comparison is statistically invalid for a variety of reasons. I analyse the key claims made by the critique. Location: Simulated data. Taxon: Simulated data. Methods: Likelihood calculations are checked by comparison between programs and by‐hand calculations, and by summing likelihoods across all possible datasets. Model adequacy of DEC versus DEC+J is checked by a simulation/inference experiment. Results: Mistakes in the critique's example likelihood calculations are demonstrated. DEC+J fits better on datasets because the DEC model is statistically inadequate in the common situation when most species have geographical ranges of single areas; the DEC model requires long residence times of multi‐area ranges, and when these are not observed, a model that does produce such data patterns, such as DEC+J, prevails. More fundamentally, statistical comparison of DEC and DEC+J produces identical log‐likelihood differences to statistical comparison of two submodels of ClaSSE where extinction rates are fixed to 0. Main Conclusions: DEC fails a basic model adequacy check for understandable reasons, while DEC+J does not. As Ree and Sanmartín recommend ClaSSE models as valid for comparison, the comparison of DEC and DEC+J is statistically valid according to their own criteria. [ABSTRACT FROM AUTHOR]

Geographically, widespread Neotropical fish lineages offer opportunities to reconstruct historical biogeography patterns and infer processes leading to modern ichthyological diversity and distribution. The characiform family Prochilodontidae is well suited for such reconstruction because their migrations limit population substructure within river systems. Therefore, their biogeographic history should match closely the history of connectivity among Neotropical river basins. Here, we combine a time‐calibrated phylogeny with biogeographic model testing to recover the history of this family's diversification. Results support the Miocene rise of the Andean Eastern Cordillera as a dispersal barrier, but also indicate a much earlier Eocene origin of the trans‐Andean genus Ichthyoelephas. Despite the early origin of the family and its three constituent genera, most prochilodontid lineages originated during the Miocene in Greater Amazonia, likely due to drainage reorganizations caused by Andean uplift. Subsequent speciation appears linked to interbasin exchanges and expansions of Amazonian lineages into Brazilian coastal systems. The modern richness of Prochilodus in easterly drainages appears to be relatively young, with only Prochilodus vimboides likely reaching that region prior to the late Miocene. The rise of the Vaupes Arch coincides with two splits between Orinocoan and Amazonian lineages circa 9 million years ago (Ma). However, two instances of later dispersal between these drainages reveal the permeability of the Vaupes Arch, suggesting that it may promote periodic speciation. This study illustrates how model‐based biogeographic studies of widespread groups can reconstruct historic paths of dispersal and help reveal how landscape evolution promoted modern diversity patterns. [ABSTRACT FROM AUTHOR]

A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees with fossil-calibrated dates. The ancestral Bombus lineage was estimated to diversify between 47.08 and 34.27 million years ago (Ma) in the Holarctic region, but largely restricted to the eastern Old World. The Neotropical region was initially colonized in the Late Miocene, where bumblebee diversification was shown to be consistent with geologic and climatic events of the Late Cenozoic. Neotropical bumblebees likely originated from Nearctic lineages, which dispersed towards South America after 29 Ma. [ABSTRACT FROM AUTHOR]

Premise: Continental‐scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species‐rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center. Methods: We used high‐throughput sequencing to generate unprecedented resolution and near complete species‐level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal. Results: Present‐day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species‐rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region. Conclusions: Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene–Miocene, shaped the present‐day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis. [ABSTRACT FROM AUTHOR]

Aim: Phenotypes promoting dispersal over ecological timescales may have macroevolutionary consequences, such as long‐distance dispersal and diversification. However, whether dispersal traits explain the distribution of pantropical plant groups remains unclear. Here we reconstruct the biogeographical history of a tree clade to assess whether seed dispersal traits and biome‐switching explain the clade's pantropical distribution. Location: Pantropical. Taxon: The Pterocarpus clade (Leguminosae/Fabaceae). Methods: We sequenced 303 nuclear loci using target capture and generated a time‐calibrated phylogenomic tree. We also generated a corroborative time‐calibrated phylogenetic tree from data‐mined Sanger‐sequencing data. We then collated distribution data and seed dispersal morphology traits to compare trait‐dependent and trait‐independent biogeographical models, allowing us to infer whether dispersal traits influenced Pterocarpus' spatio‐temporal evolution. Finally, using the results of these model tests, we estimated the ancestral ranges and biomes of Pterocarpus species to better understand their biogeographical history, and assessed the degree and direction of biome‐switching over the course of their diversification. Results: We recovered well‐supported phylogenetic relationships within Pterocarpus, within which there were two subclades – one neotropical and the other palaeotropical. Our divergence date estimates suggested that Pterocarpus diversified from around 12 Ma, during the Miocene. Trait‐dependent biogeographical models were rejected for both range and biome evolution within Pterocarpus, but models including dispersal were supported. Pterocarpus' ancestral node shared a range across the new‐world and old‐world tropics, followed by divergence into palaeotropical and neotropical clades. Biome‐switching occurred most frequently into rainforest and grassland. Main conclusions: Our analyses suggest that Pterocarpus underwent infrequent cross‐continental dispersal and establishment into novel biomes. While this was minimally impacted by seed dispersal traits, biome‐switching following long‐distance dispersal and climate change have played an important role in diversification within Pterocarpus since the Miocene. Indeed, rare events of long‐distance dispersal likely explain the wide distributions of many pantropical plant species. [ABSTRACT FROM AUTHOR]

Nisusiidae is a rhynchonelliform brachiopod family that was widely distributed in low‐latitude regions during the middle Cambrian (Stage 3 of Series 2 to the Drumian Stage of the Miaolingian Series). Cladistic analysis of 24 nisusiid species including two species from South Korea (Nisusia paucicostellata and Nisusiidae gen. et sp. indet.) demonstrates that the nisusiids consist of two sister clades (Clade 1 and 2) whose common ancestor was derived from a paraphyletic 'basal' group. Non‐spinose taxa are all included in Clade 1, while spinose Nisusia species are found throughout the three groups including Clade 1, indicating paraphyly of Nisusia. The optimized ancestral area(s) are assigned to internal nodes of the taxon area cladogram using both the Fitch algorithm and the DIVALIKE+J model of BioGeoBEARS, and then the relationship between cladogenetic area transition types and palaeogeographical areas is examined using the 'area‐transition count' method. Of 10 possible cladogenetic area transitions, which are combinations of range contraction (C), expansion (E), switch (S) and no range change (N), six (CC, CE, CN, EN, NN and NS) are observed in the two optimization results. It is proposed that the nisusiids originated in Laurentia as a strongly spinose form and dispersed into high‐latitude peri‐Gondwana during Stage 3 and then strongly diversified into other areas during Stage 4, and that non‐spinose forms evolved later, mainly in Laurentia. The nisusiid palaeobiogeographical pattern is interpreted to reflect distributional range changes that were probably caused by palaeo‐oceanic currents with the aid of island arcs as stepping stones, and pumice, produced by volcanic activity, as the means of dispersal. [ABSTRACT FROM AUTHOR]

Abstract Background The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. Results Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of ‘reverse’ dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. Conclusions Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing.

Aim: Cosmopolitan distributions have classically been explained by Pangaean vicariance. However, evidence of recently diverged cosmopolitan groups has re‐opened consideration on the processes involved. Our aim is to estimate the processes leading to the worldwide distribution of the kleptoparasitoid genus Ceropales. Location: Worldwide. Taxon: Ceropales spider wasps (Pompilidae). Methods: Data from three molecular markers for 52 specimens of Ceropales and two calibration points from previous analyses were used to reconstruct a dated phylogeny under a relaxed molecular clock. We compared the fit of 12 models using BioGeoBEARS: DEC (subset sympatry, narrow vicariance), DIVALIKE (narrow and wide vicariance), BAYAREALIKE (widespread sympatry), and these same models with an added jump dispersal parameter and constraining dispersal rates among areas. Using the AIC best‐fit model (DEC+J), we performed Biogeographic Stochastic Mapping (BSM) to infer biogeographic processes by simulating 200 BSM on the BEAST chronogram. Results: The origin of crown‐group Ceropales was ca. 10.6 Ma (15.7–6.5 95% HPD), and 11 jump‐dispersal events explain its distribution. A constrained DEC+J model, allowing adjacent area dispersal was the best‐fit AIC model. Dispersals across the Bering land bridge, Isthmus of Panama, Mediterranean Sea, and Sunda Plains took place from the late Miocene to present times. Main conclusions: Ceropales is a recently diverged group that originated in Eurasia in the Miocene and dispersed to occupy the Americas, Africa, and Australia. Colonization was probably favored by the already diversified hosts (Pompilinae and Pepsinae), which reduced limiting factors such as food resource and nest construction. The evolution of a generalist parasitic lifestyle could facilitate long‐distance dispersal. This is the first study addressing the global historical biogeography of a cosmopolitan spider wasp. [ABSTRACT FROM AUTHOR]

Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere (‘out-of-India’ hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.

The Andes is recognized as one of the most biodiverse places on Earth, promoting in its uplift process a series of recent rapid diversification events in different biotic groups like birds, mammals, insects and vascular plants. The uplift of the Andes during the Cenozoic acted as a barrier for many biotic groups, as a scenario for radiation processes due to occupancy of different niches and as a corridor for others. Connections between the Andes and the Atlantic Forest showed intermittent phases along the Cenozoic, affecting the distribution patterns and diversification of different biotic groups. Nowadays, the Andes and the Atlantic Forest are both considered globally relevant biodiversity hotspots. Floristic groups thriving in both hotspots are crucial for a better understanding of their biogeographic history, as well as for informing future conservation actions. Mutisia (Asteraceae), a genus comprising 63 perennial shrubs and vines endemic to South America, shows a marked West-East disjunction: Most species occupy almost the whole Andean chain from Colombia to Patagonia, while a second group encompasses four species distributed in eastern Brazil and the surrounding areas of Paraguay, Uruguay and Argentina. We reconstructed the phylogeny of the genus to assess its possible biogeographic history. We analysed three DNA regions, i.e. the chloroplast trnL-trnF intergenic spacer and the nuclear ribosomal internal and external transcribed spacers, ITS and ETS. Using maximum likelihood and Bayesian inference, gene trees were reconstructed, and a concatenated phylogenetic tree was inferred. Divergence times were estimated by means of BEAST, and the ancestral areas were inferred using BioGeoBEARS. An ancestral reconstruction of morphological traits was also performed, as well as maps representing current richness hotspots within the genus. Phylogenetic analyses strongly support the monophyly of Mutisia, with two well-supported main clades: clade A, with presence of Atlantic-central-northern Andes species, and clade B, with central/southern Andes species. Dating analyses suggest that a main clade separation occurred at the early Miocene, followed by the separation of the Atlantic clade A2 by the late Miocene, and more recent radiations occurred in the central, northern and southern Andes during the Pliocene. Results are in tune with other angiosperm taxa that also underwent rapid radiations, possibly related to environmental and pollinator changes. The biogeographic history of Mutisia is related to morphological adaptations, history and geographic factors acting since the Miocene along the Andes and adjacent areas. Threat assessments and conservation actions for the genus shall include the whole distribution range, including low-range northern and southern Andes species, as well as the distinctive Atlantic Forest clade. [ABSTRACT FROM AUTHOR]

Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, mat K, ndh F, and rbc L to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum , Miersia , Solaria , and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2 n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution. [ABSTRACT FROM AUTHOR]

Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (“+J”) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation.

Aim: Islands provide opportunities for isolation and speciation. Many landmasses in the Indo‐Australian Archipelago (IAA) are oceanic islands, and founder‐event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. Location: Australasia, Indo‐Australian Archipelago, Madagascar, Pacific Islands. Taxon: Pteropus (Pteropodidae). Methods: To infer the biogeographic history of Pteropus, we sequenced up to 6,169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognized Pteropus species and subspecies with three Acerodon outgroups using BEAST and subsequently estimated ancestral areas using models implemented in BioGeoBEARS. Results: Species‐level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor with Acerodon; founder‐event speciation out of Wallacea was a common inference. Pteropus species in Micronesia and the western Indian Ocean were also inferred to result from founder‐event speciation. Main conclusions: Dispersal between regions of the IAA and the islands found therein fostered diversification of Pteropus throughout the IAA and beyond. Dispersal in Pteropus is far higher than in most other volant taxa studied to date, highlighting the importance of inter‐island movement in the biogeographic history of this large clade of large bats. [ABSTRACT FROM AUTHOR]

Background: The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. Results: Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of 'reverse' dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. Conclusions: Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing. [ABSTRACT FROM AUTHOR]

The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade's historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses. [ABSTRACT FROM AUTHOR]

Aim: Almost half of the extant species of Crocodylia (nine genera, sensu Benton & Clark) belong to the genus Crocodylus, which originated in the Miocene. Today, this genus has a circumtropical distribution, with representatives found in Asia, Oceania, Africa and the Neotropics. However, its geographical origin and the historical events behind its rapid diversification and global radiation are still debated. Here, we inferred the evolution of a set of life traits that aid in dispersal and how they influenced the biogeography of Crocodylus. Location: Global. Time period: Cretaceous to the present. Major taxa studied: Crocodylidae. Methods: We estimated biogeographical history on a published phylogeny using probabilistic biogeography models. Next, we identified four life traits likely to promote range expansion and used a trait‐based dispersal model jointly to infer evolution of these traits and their influence on the dispersal of crocodilians. Finally, we used diversification analyses to identify shifts in diversification rates. Results: An Asian origin was reconstructed for Crocodylus. Despite the small size of the phylogeny, statistical model comparison reports substantially improved the model fit of trait‐dependent over trait‐independent dispersal models. In individual tests, the four life traits considered (salt tolerance, large size, large clutches and habitat generalism) appear to be correlated statistically with higher dispersal probabilities. However, the traits are likely to be correlated with each other, and we hypothesize that they all reflect the gradual evolution of a range‐expansion phenotype in early Crocodylus that resulted in increased diversification of the clade. Main conclusions: Increased dispersal in the genus Crocodylus was associated with the gradual evolution of a range‐expansion phenotype. Interestingly, the evolution of the range‐expansion phenotype was also associated with the diversification of the genus in a period of global crocodilian extinction, indicating that range expansion might have served as a potential driver of speciation. This suggests that the concept of "spatial sorting", normally applied at the population genetic level at the leading edge of an expanding population, might also act on a macroevolutionary scale. [ABSTRACT FROM AUTHOR]

• The subfamily Rimulinae is recognized for Rimula , sister group to all other fissurellids. • Many emarginuline genera are recovered in Zeidorinae (previously Hemitominae). • Emarginula , Diodora , Fissurella are not monophyletic and need systematic revision. • Crown fissurellids originated ca. 175 Ma in the Tethys Sea curr. Indo-West Pacific. • The Atlantic was colonized via the Tethys Seaway, serving as source for further dispersal. Fissurellidae are marine gastropods with a worldwide distribution and a rich fossil record. We integrate molecular, geographical and fossil data to reconstruct the fissurellid phylogeny, estimate divergence times and investigate historical routes of oceanic dispersal. With five molecular markers for 143 terminals representing 27 genera, we resolve deep nodes and find that many genera (e.g., Emarginula , Diodora , Fissurella) are not monophyletic and need systematic revision. Several genera classified as Emarginulinae are recovered in Zeidorinae. Future work should prioritize emarginuline genera to improve understanding of ancestral traits and the early evolution of fissurellids. Tree calibration with the fossilized birth-death model indicates that crown fissurellids originated around 175 Ma, and generally resulted in younger ages for the earliest nodes than the node dating approach. Model-based biogeographic reconstruction, supported by fossils, infers an Indo-West Pacific origin, with a westward colonization of new oceans via the Tethys Seaway upon the breakup of Pangea. Western Atlantic clades then served as source for dispersal towards other parts of the globe. As the sister group to all other fissurellids, Rimula is ranked in its own subfamily, Rimulinae stat. nov. New synonyms: Hemitominae syn. nov. of Zeidorinae stat. nov. ; Cranopsis syn. nov. of Puncturella ; Variegemarginula syn. nov. of Montfortula. [ABSTRACT FROM AUTHOR]

Dinosaurs were ubiquitous in terrestrial ecosystems through most of the Mesozoic and are still diversely represented in the modern fauna in the form of birds. Recent efforts to better understand the origins of the group have resulted in the discovery of many new species of early dinosaur and their closest relatives (dinosauromorphs). In addition, recent re‐examinations of early dinosaur phylogeny have highlighted uncertainties regarding the interrelationships of the main dinosaur lineages (Sauropodomorpha, Theropoda and Ornithischia), and questioned the traditional hypothesis that the group originated in South Gondwana and gradually dispersed over Pangaea. Here, we use an historical approach to examine the impact of new fossil discoveries and changing phylogenetic hypotheses on biogeographical scenarios for dinosaur origins over 20 years of research time, and analyse the results in the light of different fossil record sampling regimes. Our results consistently optimize South Gondwana as the ancestral area for Dinosauria, as well as for more inclusive clades including Dinosauromorpha, and show that this hypothesis is robust to increased taxonomic and geographic sampling and divergent phylogenetic results. Our results do not find any support for the recently proposed Laurasian origin of dinosaurs and suggest that a southern Gondwanan origin is by far the most plausible given our current knowledge of the diversity of early dinosaurs and non‐dinosaurian dinosauromorphs. [ABSTRACT FROM AUTHOR]

Premise of the Study: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia. Methods: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. Key Results: A well‐resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. Conclusions: Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia. [ABSTRACT FROM AUTHOR]

The Late Jurassic Tendaguru Formation of Tanzania, southeastern Africa, records a rich sauropod fauna, including the diplodocoids Dicraeosaurus and Tornieria, and the brachiosaurid titanosauriform Giraffatitan. However, the taxonomic affinities of other sympatric sauropod taxa are poorly understood. Here, we critically reassess and redescribe these problematic taxa, and present the largest phylogenetic analysis for sauropods (117 taxa scored for 542 characters) to explore their placement in Eusauropoda. Janenschia robusta has played a prominent role in discussions of titanosaur origins, with various authors referring at least some remains to Titanosauria, a clade otherwise known only from the Cretaceous. Redescription of the holotype of Janenschia, and all referable remains, supports its validity and placement as a non-neosauropod eusauropod. It forms a clade with Haestasaurus from the earliest Cretaceous of the UK, and the Middle/Late Jurassic Chinese sauropod Bellusaurus. Phylogenetic analysis and CT scans of the internal pneumatic tissue structure of Australodocus bohetii tentatively support a non-titanosaurian somphospondylan identification, making it the only known pre-Cretaceous representative of that clade. New information on the internal pneumatic tissue structure of the dorsal vertebrae of the enigmatic Tendaguria tanzaniensis, coupled with a full redescription, results in its novel placement as a turiasaur. Tendaguria is the sister taxon of Moabosaurus, from the Early Cretaceous of North America, and is the first turiasaur recognized from Gondwana. A previously referred caudal sequence cannot be assigned to Janenschia and displays several features that indicate a close relationship with Middle–Late Jurassic East Asian mamenchisaurids. It can be diagnosed by six autapomorphies, so we erect the new taxon Wamweracaudia keranjei gen. et sp. nov. The presence of a mamenchisaurid in the Late Jurassic of southern Gondwana indicates an earlier and more widespread diversification of this clade than previously realized, prior to the geographic isolation of East Asia. Our revised phylogenetic dataset sheds light on the evolutionary history of Eusauropoda, including supporting a basal diplodocoid placement for Haplocanthosaurus, and elucidating the interrelationships of rebbachisaurids. The Tendaguru Formation shares representatives of nearly all sauropod lineages with Middle Jurassic–earliest Cretaceous global faunas, but displays a greater range of diversity than any of those faunas considered individually. Biogeographic analysis indicates that the Tendaguru sauropod fauna was assembled as a result of three main phenomena during the late Early and/or Middle Jurassic: (1) invasions from Euramerica (brachiosaurids, turiasaurs); (2) endemism in west Gondwana (dicraeosaurids, diplodocids); and (3) regional extinctions that restricted the ranges of once widespread groups (mamenchisaurids, the Janenschia lineage). Multiple dispersals across the Central Gondwanan Desert are required to explain the distributions of Jurassic sauropods, suggesting that this geographic feature was at most a filter barrier that became easier to cross during the late Middle Jurassic. [ABSTRACT FROM AUTHOR]

Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat‐forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool‐or cold‐climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates. This study tests the hypothesis that Sphagnum (peat mosses) initially diversified at high latitudes of the Northern Hemisphere and later extended their ranges to tropical and Southern Hemisphere regions. The ancestral geographic area for the genus as a whole is ambiguous, but the four major subgenera, comprising some 90% of the generic species diversity, unambiguously originated at high latitudes. Sphagnum provides a model for research on genomic, ecological, and morphological changes associated with adaptation to warm climates from cold or cool climate ancestors. [ABSTRACT FROM AUTHOR]

Abstract: Titi monkeys, subfamily Callicebinae, are a diverse, species‐rich group of Neotropical primates with an extensive range across South America. Their distribution in space and time makes them an interesting primate model for addressing questions of Neotropical historical biogeography. Our aim was to reconstruct the biogeographic history of Callicebinae to better understand their diversification patterns and the history of their colonisation of South America since the late Miocene. We reconstructed a time‐calibrated phylogeny of 19 titi species under Bayesian inference using two mitochondrial and 11 nuclear loci. Species were assigned across eight Neotropical areas of endemism, and statistical biogeographic methods implemented in BioGeoBEARS were employed to estimate ancestral areas using 12 biogeographic models. Our results indicate that the most recent common ancestor to extant titi monkeys was widespread from the present‐day Andean foothills in the Colombian Amazon, through the wet and dry savannas of Bolivia and Brazil, to the southern Atlantic forest of eastern Brazil. Genus‐level divergences were characterised by vicariance of ancestral range in the late Miocene. Species‐level diversification in Cheracebus and the Plecturocebus moloch group occurred as they spread across the Amazon in the Pleistocene and were largely characterised by a sequential, long‐distance “island‐hopping” dispersal model of speciation from a narrow area of origin through jump dispersal across rivers. This study comprises the first large‐scale investigation of the evolutionary history of titi monkeys in the context of Amazonian and South American historical biogeography and sheds light on the processes that generated the great diversity found among Callicebinae. [ABSTRACT FROM AUTHOR]

The ‘out of Australia’ hypothesis describes taxa with ancestors present on the Australian continent before the contact of the Australian plate with Southeast Asia and the subsequent biological interchange between these regions across Wallacea. Our study supports the ‘out of Australia’ hypothesis for the tropical tree genus Alphitonia and its closest relatives. A common ancestor of the entire clade inhabited Australia in the Miocene, and westward dispersal into Wallacea, the Philippines and the Asian continent was reconstructed to be of Quaternary origin. Furthermore, our study supports the currently applied taxonomy in Alphitonia and related genera, although it highlights potentially underestimated diversity. Finally, our study highlights the need for further investigations in Alphitonia and related genera and for including fossil-rich related taxa. The need for these investigations also arises from a potential human-mediated dispersal of Alphitonia spp. in Polynesia, which cannot be clearly proven by our approach. [ABSTRACT FROM AUTHOR]

Darwin's finches are considered a classic example of an adaptive radiation, and have been the focus of numerous studies from ecological and evolutionary perspectives. Few studies, however, have attempted to investigate the biogeographic origins of Darwin's finches. In this paper, we reconstruct the ancestral biogeography of Coerebinae, the tanager subfamily that contains Darwin's finches and their 14 closest relatives. We use this reconstruction to examine the origin of Darwin's finches, and the diversification of this clade of tanagers. We test multiple biogeographic models using the R package BioGeoBEARS utilizing a recent multilocus phylogeny. We used these models to examine 2 different hypotheses regarding the biogeographic origin of Darwin's finches. The majority of ancestral ranges within this subfamily were estimated as Caribbean restricted. Biogeographic models run using 8 regions suggest Darwin's finches arose from a long-distance dispersal event from the Caribbean Islands as opposed to the geographically closer mainland South America. However, models run using only 5 areas suggest equal probability between a Caribbean and a mainland South America origin to Darwin's finches. This study suggests equal probability for a Caribbean origin to Darwin's finches as a South American mainland origin. Conflict between models run using different biogeographic regimes highlights the sensitivity of these reconstructions to biogeographic region delineation. Overall, the Caribbean Islands appear especially important for the initial diversification of this clade, with many small-island restricted species diversifying early in the radiation. Colonization success was likely coupled with high dispersal ability and highly variable bill morphology to exploit vacant niche space. [ABSTRACT FROM AUTHOR]

Species richness is not evenly distributed across the tree of life and a limited number of lineages comprise an extraordinarily large number of species. In lichen-forming fungi, only two genera are known to be ‘ultradiverse’ (>500 species), with the most diverse genus, Xanthoparmelia, consisting of c. 820 species. While Australia and South Africa are known as current centres of diversity for Xanthoparmelia, it is not well known when and where this massive diversity arose. To better understand the geographical and temporal context of diversification in this diverse genus, we sampled 191 Xanthoparmelia specimens representing c. 124 species/species-level lineages from populations worldwide. From these specimens, we generated a multi-locus sequence data set using Sanger and high-throughput sequencing to reconstruct evolutionary relationships in Xanthoparmelia, estimate divergence times and reconstruct biogeographical histories in a maximum likelihood and Bayesian framework. This study corroborated the phylogenetic placement of several morphologically or chemically diverse taxa within Xanthoparmelia, such as Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Omphalodiella, Paraparmelia, Placoparmelia and Xanthomaculina, in addition to improved phylogenetic resolution and reconstruction of previously unsampled lineages within Xanthoparmelia. Our data indicate that Xanthoparmelia most likely originated in Africa during the early Miocene, coinciding with global aridification and development of open habitats. Reconstructed biogeographical histories of Xanthoparmelia reveal diversification restricted to continents with infrequent intercontinental exchange by long-distance dispersal. While likely mechanisms by which Xanthoparmelia obtained strikingly high levels of species richness in Australia and South Africa remain uncertain, this study provides a framework for ongoing research into diverse lineages of lichen-forming fungi. Finally, our study highlights a novel approach for generating locus-specific molecular sequence data sets from high throughput metagenomic reads. [ABSTRACT FROM AUTHOR]

The family Margaritiferidae encompasses 12 valid species, which are distributed widely but disjunctively in the Northern Hemisphere. A lack of a well resolved and temporally calibrated phylogenetic framework of Margaritiferidae has made it difficult to discuss the evolutionary pattern and process. Phylogenetic relationships between five major clades, which were revealed in earlier studies, remain elusive and unresolved. Lamprotula rochechouartii has long been classified within the family Unionidae based on shell morphology, but our preliminary molecular study on this species made us hypothesize that it has an affinity with margaritiferids. Hence, five loci (COI, 16S, 18S, 28S and histone H3) were used to investigate the phylogenetic position of L. rochechouartii and intra-familial relationships within Margaritiferidae using various partitioning strategies. Moreover, two mitochondrial genomes were newly obtained to further resolve and validate the five-clade relationships within Margaritiferidae in a broad view of Unionoida evolution. Both five-gene and mitogenome datasets strongly advocated treating Lamprotula rochechouartii as Margaritifera rochechouartii comb . nov . Maximum likelihood and Bayesian inference analyses using partitioned five-gene dataset resulted in various topologies, but five well-supported clades were obtained. The most probable cladistic relationships generated by five-gene dataset analyses were identical to subsequent whole mitogenome analyses except the position of M. monodonta . M. rochechouartii and M. laosensis had a well-supported sister relationship and formed a basal clade splitting from the rest of the family. Based on six reliable fossils, crown age of the extant Margaritiferidae was estimated during the Late Cretaceous at 88.3 Ma (95% HPD = 66.2–117.4). But we hypothesized a much earlier origin of this family due to the Permian stem age (mean = 257 Ma, 95% HPD = 230.0–296.0) and a high extinction rate in the whole order. Biogeographic scenarios supported a Laurasian origin of extant Margaritiferidae during the Late Cretaceous, and suggested that Asian margaritiferids may have had two origins, having either Asia ( M. rochechouartii, M. laosensis ) or North America ( M. dahurica, M. laevis, and M. middendorffi ) as ancestral. The newly added Margaritiferidae species M. rochechouartii expands our recognized distribution range of modern margaritiferids. Our results indicate that whole mitogenome sequences can be used to reconstruct robust phylogenetic relationships for freshwater mussels, especially with the help of adding M-type mitogenomes. [ABSTRACT FROM AUTHOR]

Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa–Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous–Palaeogene or the Eocene–Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.

The Middle to Late Ordovician was a time of profound biotic diversification, paleoecological change, and major climate shifts. Yet studies examining speciation mechanisms and drivers of dispersal are lacking. In this study, we use Bayesian phylogenetics and maximum likelihood analyses in the R package BioGeoBEARS to reanalyze ten published data matrices of brachiopods and trilobites and produce time-calibrated species-level phylogenetic hypotheses with estimated biogeographic histories. Recovered speciation and biogeographic patterns were examined within four time slices to test for changes in speciation type across major tectonic and paleoclimatic events. Statistical model comparison showed that biogeographic models that incorporate long-distance founder-event speciation best fit the data for most clades, which indicates that this speciation type, along with vicariance and traditional dispersal, were important for Paleozoic benthic invertebrates. Speciation by dispersal was common throughout the study interval, but notably elevated during times of climate change. Vicariance events occurred synchronously among brachiopod and trilobite lineages, indicating that tectonic, climate, and ocean processes affected benthic and planktotrophic larvae similarly. Middle Ordovician inter-oceanic dispersal in trilobite lineages was influenced by surface currents along with volcanic island arcs acting as “stepping stones” between areas, indicating most trilobite species may have had a planktic protaspid stage. These factors also influenced brachiopod dispersal across oceanic basins among Laurentia, Avalonia, and Baltica. These results indicate that gyre spin-up and intensification of surface currents were important dispersal mechanisms during this time. Within Laurentia, surface currents, hurricane tracks, and upwelling zones controlled dispersal among basins. Increased speciation during the Middle Ordovician provides support for climatic facilitators for diversification during the Great Ordovician Biodiversification Event. Similarly, increased speciation in Laurentian brachiopod lineages during the Hirnantian indicates that some taxa experienced speciation in relation to major climate changes. Overall, this study demonstrates the substantial power and potential for likelihood-based methods for elucidating biotic patterns during the history of life. [ABSTRACT FROM AUTHOR]

Mexican dry environments are widespread and characterized by a rich flora and fauna in terms of both overall species diversity and endemism, but the factors that have shaped this diversity remain unclear. In this study, we evaluated hypotheses concerning the biogeographical origin and evolutionary history of Florestina (Asteraceae) in Mexican dry environments. For this, we generated a time-calibrated phylogenetic tree from the nuclear non-coding external and and internal transcribed spacers (ETS, ITS), using the program BEAST. Based on this phylogenetic tree, we employed the package BioGeoBEARS to infer the historical biogeography of the genus, comparing different biogeographical models and estimating the ancestral range probabilities. Our time-calibrated phylogenetic tree suggested that the genus Florestina diverged during the early Pliocene c. 5.2 Mya and diversification continued throughout the Pleistocene. Furthermore, results suggest that the biogeographical origin of the Hymenothrix/Palafoxia/Florestina clade was in Nearctic regions, not in Neotropical regions as previously suggested. We hypothesize that the ancestor of Florestina became disjunct and isolated in tropical dry forests of southern Mexico from Palafoxia after the rifting of the Baja California peninsula from the Mexican mainland. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. METHODS: Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. KEY RESULTS: A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. CONCLUSIONS: Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships and biogeographic history of Caribbean island ameivas ( Pholidoscelis) are not well-known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well-supported phylogeny and assess historical colonization patterns in the group. We obtained sequence data from 316 nuclear loci and one mitochondrial marker for 16 of 19 extant species of the Caribbean endemic genus Pholidoscelis. Phylogenetic analyses were carried out using both concatenation and species tree approaches. To estimate divergence times, we used fossil teiids to calibrate a timetree which was used to elucidate the historical biogeography of these lizards. All phylogenetic analyses recovered four well-supported species groups (clades) recognized previously and supported novel relationships of those groups, including a ( P. auberi + P. lineolatus) clade (western + central Caribbean), and a ( P. exsul + P. plei) clade (eastern Caribbean). Divergence between Pholidoscelis and its sister clade was estimated to have occurred ~25 Ma, with subsequent diversification on Caribbean islands occurring over the last 11 Myr. Of the six models compared in the biogeographic analyses, the scenario which considered the distance among islands and allowed dispersal in all directions best fit the data. These reconstructions suggest that the ancestor of this group colonized either Hispaniola or Puerto Rico from Middle America. We provide a well-supported phylogeny of Pholidoscelis with novel relationships not reported in previous studies that were based on significantly smaller datasets. We propose that Pholidoscelis colonized the eastern Greater Antilles from Middle America based on our biogeographic analysis, phylogeny, and divergence time estimates. The closing of the Central American Seaway and subsequent formation of the modern Atlantic meridional overturning circulation may have promoted dispersal in this group. [ABSTRACT FROM AUTHOR]

Despite their complex evolutionary history and the rich fossil record, the higher level phylogeny and historical biogeography of living turtles have not been investigated in a comprehensive and statistical framework. To tackle these issues, we assembled a large molecular dataset, maximizing both taxonomic and gene sampling. As different models provide alternative biogeographical scenarios, we have explicitly tested such hypotheses in order to reconstruct a robust biogeographical history of Testudines. We scanned publicly available databases for nucleotide sequences and composed a dataset comprising 13 loci for 294 living species of Testudines, which accounts for all living genera and 85% of their extant species diversity. Phylogenetic relationships and species divergence times were estimated using a thorough evaluation of fossil information as calibration priors. We then carried out the analysis of historical biogeography of Testudines in a fully statistical framework. Our study recovered the first large-scale phylogeny of turtles with well-supported relationships following the topology proposed by phylogenomic works. Our dating result consistently indicated that the origin of the main clades, Pleurodira and Cryptodira, occurred in the early Jurassic. The phylogenetic and historical biogeographical inferences permitted us to clarify how geological events affected the evolutionary dynamics of crown turtles. For instance, our analyses support the hypothesis that the breakup of Pangaea would have driven the divergence between the cryptodiran and pleurodiran lineages. The reticulated pattern in the ancestral distribution of the cryptodiran lineage suggests a complex biogeographic history for the clade, which was supposedly related to the complex paleogeographic history of Laurasia. On the other hand, the biogeographical history of Pleurodira indicated a tight correlation with the paleogeography of the Gondwanan landmasses. [ABSTRACT FROM AUTHOR]

Aim Our aim was to examine gracile capuchin ( Cebus) and robust capuchin monkey ( Sapajus) diversification, with a focus on recent Sapajus expansion within Amazonia. We wanted to reconstruct the biogeographical history of the clade using statistical methods that model lineages' occupation of different regions over time in order to evaluate recently proposed 'Out of Amazonia' and 'Reinvasion of Amazonia' hypotheses as alternative explanations for the extensive geographical overlap between reciprocally monophyletic gracile ( Cebus) and robust ( Sapajus) capuchin monkeys. Location Central and South America. Methods We reconstructed a time-calibrated molecular phylogeny for capuchins under Bayesian inference from three mitochondrial genes. We then categorized 12 capuchin clades across four Neotropical centres of endemism and reconstructed the biogeographical history of the capuchin radiation using six models implemented in 'BioGeo BEARS'. We performed a phylogeographical analysis for a robust capuchin clade that spans the Atlantic Forest, Cerrado, Caatinga and Amazonia. Results We find support for a late Miocene vicariant Cebus-Sapajus divergence and a Pleistocene Sapajus invasion of Amazonia from the Atlantic Forest. Our new analyses confirm Sapajus diversified first in the Atlantic Forest, with subsequent range expansion into widespread sympatry with Cebus in Amazonia, as well as multiple expansions into drier savanna-like habitats. We do not find mitochondrial molecular congruence with morphological species distinctions for Sapajus flavius, S. cay, S. macrocephalus, S. libidinosus and S. apella; instead, these five morphological types together form a single widespread clade (Bayesian posterior probability = 1) with geographical substructure and shared ancestry during the Pleistocene. Main conclusions Our results support vicariance dividing ancestral capuchin populations in Amazonia versus the Atlantic Forest, and a Pleistocene 'Amazonian invasion' by Sapajus to explain the present-day sympatry of Cebus and Sapajus. [ABSTRACT FROM AUTHOR]