Diversity dynamics of Zosterophyllopsida

The Zosterophyllopsida were major contributors to the diversification of early land plants. We present the first detailed analysis of the diversity dynamics of these plants from an updated database of all currently recognized zosterophyllopsid species. A set of quantitative methods classically used in palaeodiversity studies was applied to two data sets. The first one, ‘Zosterophyllopsida sensu stricto’, corresponds to the clade identified by Hao & Xue (The Early Devonian Posongchong Flora of Yunnan. (2013), Science Press). In the second, called ‘Zosterophyllopsida sensu lato’, barinophytalean‐type plants and taxa for which zosterophyllopsid affinities are suspected are added. The number of localities is used to explore sampling bias. Results show that sampling effect is minimal for the Early Devonian. For this time interval, both data sets record consistent patterns of changes suggesting that, whatever their affinities, all taxa included in the Zosterophyllopsida sensu lato show similar evolutionary trends. The diversity dynamics of zosterophyllopsids are characterized by a radiation during the Lochkovian, maximal values in the Pragian and a decline starting in the Emsian. The proportion of zosterophyllalean taxa with terminal sporangia is high until the Late Lochkovian when gosslingialean taxa without terminal sporangia evolved. During the Middle and Late Devonian, when diversity patterns are strongly affected by sampling, zosterophyllopsid diversity is low and characterized by a high proportion of barinophytacean and gosslingialean taxa, the latter becoming extinct in the Early Frasnian.     

Ostracods had colonized estuaries by the late Silurian

The fossil record of terrestrialization documents notable shifts in the environmental and physiological tolerances of many animal and plant groups. However, for certain significant components of modern freshwater and terrestrial environments, the transition out of marine settings remains largely unconstrained. Ostracod crustaceans occupy an exceptional range of modern aquatic environments and are invaluable palaeoenvironmental indicators in the fossil record. However, pre-Carboniferous records of supposed non-marine and marginal marine ostracods are sparse, and the timing of their marine to non-marine transition has proven elusive. Here, we reassess the early environmental history of ostracods in light of new assemblages from the late Silurian of Vietnam. Two, low diversity but distinct ostracod assemblages are associated with estuarine deposits. This occurrence is consistent with previous incidental reports of ostracods occupying marginal and brackish settings through the late Silurian and Devonian. Therefore, ostracods were pioneering the occupation of marginal marine and estuarine settings 60 Myr before the Carboniferous and they were a component of the early phase of transition from marine to non-marine environments.     

Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory

The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.     

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter‐ and intraspecific diversification. Location Mexico, Guatemala, and the western United States. Methods We combined range‐wide sampling (67 individuals representing three putative species distributed across northern Middle America and western North America) and phylogenetic analyses of 1637 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times. The hypothesized concordance of inferred gene trees with geological histories was assessed using topology tests. Results We identified three major lineages of Middle American gophersnakes, and strong phylogeographical structure within each lineage. Gene trees were statistically congruent with hypothesized geological histories for two of the three postulated geological events. Estimated divergence dates and the geographical distribution of genetic variation further support mixed responses to these geological events. Considerable phylogeographical structure appears to have been generated during the Pleistocene. Main conclusions Phylogenetic and phylogeographical structure in gophersnakes distributed across northern Middle America and western North America highlights the influence of both Neogene vicariance events and Pleistocene climate change in shaping genetic diversity in this region. Despite the presence of two major geographical barriers in southern Mexico, extreme geological and environmental heterogeneity in this area may have differentially structured genetic diversity in highland taxa. To the north, co‐distributed taxa may display a more predictable pattern of diversification across the warm desert regions. Future studies should incorporate nuclear data to disentangle inferred lineage boundaries and further elucidate patterns of mitochondrial introgression.     

INVESTIGATING PROCESSES OF NEOTROPICAL RAIN FOREST TREE DIVERSIFICATION BY EXAMINING THE EVOLUTION AND HISTORICAL BIOGEOGRAPHY OF THE PROTIEAE (BURSERACEAE)

Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of Neotropical trees. Bayesian fossil‐calibrated analyses date the Protieae stem at 55 Mya. Biogeographic analyses reconstruct an initial late Oligocene/early Miocene radiation in Amazonia for Neotropical Protieae, with several subsequent late Miocene dispersal events to Central America, the Caribbean, Brazil's Atlantic Forest, and the Chocó. Regional phylogenetic structure results indicate frequent dispersal among regions throughout the Miocene and many instances of more recent regional in situ speciation. Habitat specialization to white sand or flooded soils was common, especially in Amazonia. There was one significant increase in diversification rate coincident with colonization of the Neotropics, followed by a gradual decrease consistent with models of diversity‐dependent cladogenesis. Dispersal, biotic interactions, and habitat specialization are thus hypothesized to be the most important processes underlying the diversification of the Protieae.     

Delayed recovery of non-marine tetrapods after the end-Permian mass extinction tracks global carbon cycle

During the end-Permian mass extinction, marine ecosystems suffered a major drop in diversity, which was maintained throughout the Early Triassic until delayed recovery during the Middle Triassic. This depressed diversity in the Early Triassic correlates with multiple major perturbations to the global carbon cycle, interpreted as either intrinsic ecosystem or external palaeoenvironmental effects. In contrast, the terrestrial record of extinction and recovery is less clear; the effects and magnitude of the end-Permian extinction on non-marine vertebrates are particularly controversial. We use specimen-level data from southern Africa and Russia to investigate the palaeodiversity dynamics of non-marine tetrapods across the Permo-Triassic boundary by analysing sample-standardized generic richness, evenness and relative abundance. In addition, we investigate the potential effects of sampling, geological and taxonomic biases on these data. Our analyses demonstrate that non-marine tetrapods were severely affected by the end-Permian mass extinction, and that these assemblages did not begin to recover until the Middle Triassic. These data are congruent with those from land plants and marine invertebrates. Furthermore, they are consistent with the idea that unstable low-diversity post-extinction ecosystems were subject to boom-bust cycles, reflected in multiple Early Triassic perturbations of the carbon cycle.     

A re-evaluation of the ‘mid-Cretaceous sauropod hiatus’ and the impact of uneven sampling of the fossil record on patterns of regional dinosaur extinction

The mid-Cretaceous of North America and Europe has long been noted for the absence of sauropod dinosaurs, leading several authors to suggest that this depauperate interval is a consequence of an end-Albian sauropod extinction. This time period has become known as the ‘mid-Cretaceous sauropod hiatus’, with the subsequent presence of titanosaurian sauropods in the latest Cretaceous of North America and Europe interpreted as the result of dispersal of taxa from South America and Africa, respectively. However, several lines of evidence indicate that this hiatus is probably a sampling artefact. New fossil and trackway discoveries have considerably shortened the hiatus, reducing it to the Turonian–early Campanian in North America, and to just two short intervals in the late Cenomanian–early Turonian and late Coniacian–Santonian of Europe. Palaeoenvironmental analyses of sauropods demonstrate an inland terrestrial preference for titanosaurs, the dominant Late Cretaceous sauropods; however, during the hiatus there was a decline in inland deposits and increase in coastal sediments in Europe and North America, which would have greatly reduced the probability of preserving titanosaurs. Neither the decline in inland deposits, nor the ‘sauropod hiatus’, occurred elsewhere in the world. Statistical comparisons also demonstrate a significant positive correlation between fluctuations in inland deposits and sauropod occurrences during the mid–Late Cretaceous in Europe and North and South America. Lastly, cladistic analyses do not place latest Cretaceous North American and European titanosaurs within South American and African clades, contradicting the predictions of the ‘austral immigrant’ hypothesis. The latter hypothesis also receives little support from biogeographical analysis of dispersal among titanosaurs. Thus, the ‘sauropod hiatus’ of North America and Europe is most plausibly interpreted as the product of a sampling bias pertaining to the rarity of inland sediments and dominance of coastal deposits preserved in these two regions during the mid-Cretaceous. The presence of titanosaurs in these areas during the latest Cretaceous can be explained by dispersal from Southern Hemisphere continents, but this is no more probable than descent from Early Cretaceous incumbent faunas or dispersal from Asia.     

Terrestrial-marine teleconnections in the Devonian: links between the evolution of land plants,weathering processes,and marine anoxic events

The Devonian Period was characterized by major changes in both the terrestrial biosphere, e.g. the evolution of trees and seed plants and the appearance of multi-storied forests, and in the marine biosphere, e.g. an extended biotic crisis that decimated tropical marine benthos, especially the stromatoporoid-tabulate coral reef community. Teleconnections between these terrestrial and marine events are poorly understood, but a key may lie in the role of soils as a geochemical interface between the lithosphere and atmosphere/hydrosphere, and the role of land plants in mediating weathering processes at this interface. The effectiveness of terrestrial floras in weathering was significantly enhanced as a consequence of increases in the size and geographic extent of vascular land plants during the Devonian. In this regard, the most important palaeobotanical innovations were (1) arborescence (tree stature), which increased maximum depths of root penetration and rhizoturbation, and (2) the seed habit, which freed land plants from reproductive dependence on moist lowland habitats and allowed colonization of drier upland and primary successional areas. These developments resulted in a transient intensification of pedogenesis (soil formation) and to large increases in the thickness and areal extent of soils. Enhanced chemical weathering may have led to increased riverine nutrient fluxes that promoted development of eutrophic conditions in epicontinental seaways, resulting in algal blooms, widespread bottomwater anoxia, and high sedimentary organic carbon fluxes. Long-term effects included drawdown of atmospheric pCO₂ and global cooling, leading to a brief Late Devonian glaciation, which set the stage for icehouse conditions during the Permo-Carboniferous. This model provides a framework for understanding links between early land plant evolution and coeval marine anoxic and biotic events, but further testing of Devonian terrestrial-marine teleconnections is needed.     

Diversity and richness of the Devonian terrestrial plants in the Southeastern Mountainous Altay (Southern Siberia): Regional versus global patterns

Devonian deposits of the Southeastern Mountainous Altay, a large region in Southern Siberia, contain abundant remains of terrestrial plants. A semi-quantitative analysis of this regional palaeobotanical record reveals how both the diversity (number of taxa) and richness (number of taxa with an account of their abundances) of floristic assemblages changed during the Emsian–early Famennian time interval. A total of 60 species, representing 42 genera, are known from 8 regional assemblages. Changes in diversity of species and genera occurred simultaneously. The number of taxa was high in the early Emsian, declined in the late Emsian, rose again in the Eifelian–middle Givetian, dropped in the late Givetian, reached the highest values in the early Frasnian, and experienced the greatest decline taking place in the late Frasnian–early Famennian. The standing diversity (number of taxa crossing the time boundaries) was maximal in the Middle Devonian. The dynamics of terrestrial plant richness was similar to that of diversity with an exception of middle Givetian decline in richness despite growth of diversity. The floras were dominated by pteridophytes. Propteridophytes were less abundant, and pinophytes were very rare. Propteridophyte extinctions were high in the middle Givetian, concurrent with a brief decline in pteridophytes. Some regional and global patterns of floral dynamics were similar. However, propteridophyte decline was not abrupt globally. The main abiotic driving factor influencing species richness and diversity appears to have been regional shoreline shifts. It does not appear that climate changes was important for regional changes in phytodiversity, although both regional and global phytodiversity was at its high during the Middle Devonian cooling phase. A comparison of palaeobotanical data from the Southeastern Mountainous Altay and Kazakhstan suggests palaeogeographic proximity and proves an idea of Altay-Mongolian terrane wandered between Gondwana, Kazakhstan, and Siberia. The early Emsian and the early Frasnian, when floras of the study region were diverse and rich, are characterized by the very high degree of similarity. Thus, interregional floral exchanges would facilitate plant radiations.     

African origin and global distribution patterns: Evidence inferred from phylogenetic and biogeographical analyses of ectomycorrhizal fungal genus Strobilomyces

Aim

The ectomycorrhizal genus Strobilomyces is widely distributed throughout many parts of the world, but its origin, divergence and distribution patterns remain largely unresolved. In this study, we aim to explore the species diversity, distribution and evolutionary patterns of Strobilomyces on a global scale by establishing a general phylogenetic framework with extensive sampling.

Location

Africa, Australasia, East Asia, Europe, North America, Central America and Southeast Asia.

Methods

The genealogical concordance phylogenetic species recognition method was used to delimit phylogenetic species. Divergence times were estimated using a Bayesian uncorrelated lognormal relaxed molecular clock. The ancestral area and host of Strobilomyces were inferred via the programs rasp and mesquite . The change of diversification rate over time was estimated using Ape, Laser and Bammtools software packages.

Results

We recognize a novel African clade and 49 phylogenetic species with morphological evidence, including 18 new phylogenetic species and 23 previously described ones. Strobilomyces probably originated in Africa, in association with Detarioideae/Phyllanthaceae/Monotoideae during the early Eocene. The dispersal to Southeast Asia can be explained by Wolfe's “Boreotropical migration” hypothesis. East Asia, Australasia, Europe and North/Central America are primarily the recipients of immigrant taxa during the Oligocene or later. A rapid radiation implied by one diversification shift was inferred within Strobilomyces during the Miocene.

Main conclusions

An unexpected phylogenetic species diversity within Strobilomyces was uncovered. The highest diversity, resulting probably from a rapid radiation, was found in East Asia. Dispersal played an important role in the current distribution pattern of Strobilomyces. The Palaeotropical disjunction is explained by species dispersal from Africa to Southeast Asia through boreotropical forests during the early Eocene. Species from the Northern Hemisphere and Australasia are largely derived from immigrant ancestors from Southeast Asia.     

A comparison of the taxonomic richness of temperate plants in East Asia and North America

The taxonomic richness of seed plants at different taxonomic levels was compared between temperate East Asia and North America at both continental and semi-continental scales. In each comparison, land area and latitude range were adjusted to a comparable level between the two continental regions. East Asia is significantly more diverse than North America. In general, differences in taxonomic diversity arise at and below the genus level. At the continental scale, East Asia has 1.3 and 1.5 times as many genera and species, respectively, as North America. The northern part of East Asia has 1.1 times as many species as the northern part of North America. At the genus level, the northern part of East Asia is less diverse than the northern part of North America by a factor of 0.94. This pattern indicates that the diversity bias between the two continental regions results from the flora of southern East Asia. The diversity differences between East Asia and North America are not homogenously distributed across different plant groups. At the species level, East Asia had significantly more species than expected in magnoliids, alismatids, Liliidae, ranunculids, and rosids and had significantly less species in the Commelinidae, Caryophyllidae, and euasterids than North America.     

Spatial phylogenetics of the North American flora

North America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.     

Historical biogeography of the Southeast Asian and Malesian tribe Dissochaeteae (Melastomataceae)

The region of Tropical Southeast Asia and the Malay Archipelago is a very appealing area for research due to its outstanding biodiversity, being one of the most species-rich areas in the world with high levels of endemism, and due to its complex geological history. The high number of species in tribe Dissochaeteae (Melastomataceae) and their tendency to narrow endemism makethe tribe an ideal group for examining biogeographic patterns. We sampled 58 accessions spread over 42 accepted and two undescribed species of the Dissochaeteae. Two nuclear (ETS, ITS) and four chloroplast regions (ndhF, psbK-psbL, rbcL, rpl16) were used for divergence time estimation and ancestral area reconstruction. Results from the molecular dating analysis suggest that the diversity of Dissochaeteae in the Southeast Asian region resulted from a South American ancestor in the late Eocene. The ancestor of the Dissochaeteae might have migrated from South America to Southeast Asia via North America and then entered Eurasia over the North Atlantic land bridge during the Eocene. The origin and early diversification of the Dissochaeteae in Southeast Asia dates back to the middle Oligocene, and most of the genera originated during the Miocene. Indochina and Borneo are most likely the area of origin for the most recent common ancestor of the Dissochaeteae and for many of the early diverging clades of some genera within Southeast Asia.     

Historical isolation,range expansion,and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum)

Abstract.— The high species diversity of aquatic and terrestrial faunas in eastern North America has been attributed to range reductions and allopatric diversification resulting from historical climate change. The role these processes may have played in speciation is still a matter of considerable debate; however, their impacts on intraspecific genetic structure have been well documented. We use mitochondrial DNA sequences to reconstruct an intraspecific phylogeny of the widespread North American spotted salamander, Ambystoma maculatum , and test whether phylogenetic patterns conform to regional biogeographical hypotheses about the origins of diversity in eastern North America. Specifically, we address the number and locations of historical refugia, the extent and patterns of postglacial colonization by divergent lineages, and the origin and affinities of populations in the Interior Highland region. Despite apparent morphological uniformity, genetic discontinuities throughout the range of this species suggest that populations were historically fragmented in at least two refugia in the southern Appalachian Mountains. The ranges of these two highly divergent clades expanded northward, resulting in two widely distributed lineages that are sympatric in regions previously proposed as suture zones for other taxa. The evolutionary history of spotted salamander populations underscores the generality of biogeographical processes in eastern North America: despite differences in population size, glacial refugia, and vagility, similar signatures of differentiation are evident among and within widespread taxa.     

Longitudinal patterns of plant diversity in the North American boreal forest

Spatial patterns of plant diversity in the North American boreal forest were examined according to three plant life forms (woody plants, herbaceous plants, and bryophytes) and two taxonomic levels (species and genus), using sixty 9-ha plots sampled in white spruce (Picea glauca (Moench) Voss) and black spruce (Picea mariana (P. Mill.) B.S.P.) ecosystems along a transcontinental transect from the Pacific coast eastwards to the Atlantic coast. The patterns of inventory diversity (represented by alpha diversity), differentiation diversity (represented by the similarity index, habitat-heterogeneity index, similarity decay rate, and length of the first axis in detrended correspondence analysis), and pattern diversity (represented by the mosaic diversity index) were assessed along the transect in both ecosystem types. At the stand level, central North America had the highest alpha diversity in terms of the number of species or genera, and western North America had a higher alpha diversity than eastern North America. At the continental scale, herbaceous plants had the highest beta diversity in terms of floristic change from the eastern to western North America, bryophytes had the lowest beta diversity, and woody plants were in the middle, regardless of ecosystem type and taxonomic level. Central North America had the lowest mosaic diversity across the boreal transect of North America. The white spruce ecosystems had a higher alpha diversity than the black spruce ecosystems regardless of plant life form, taxonomic level and geographic location. The white spruce ecosystems tended to have more bryophytes, less woody plants, and higher species:genus ratio than the black spruce ecosystems. In general, the white spruce and black spruce ecosystems shared the same patterns in diversity changes at different spatial scales, plant life forms, and taxonomic levels across the transect studied. The existing patterns of plant diversity in the North American boreal forest area resulted from a combination of ecological processes and spatial configuration.     

Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists

Recent studies show that soil eukaryotic diversity is immense and dominated by micro‐organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro‐organisms. Major diversification events in multicellular organisms have often been attributed to long‐term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum‐dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro‐organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.     

Completeness of the fossil record and the validity of sampling proxies at outcrop level

Abstract: Most studies of the adequacy of the fossil record have been carried out at a global or continental scale, and they have used sampling proxies that generally do not incorporate all aspects of sampling (i.e. rock volume, accessibility, effort). Nonetheless, such studies have identified positive correlations between apparent diversity and various sampling proxies. The covariation of fossil and rock record signals has been interpreted as evidence for bias or for a common cause, such as sea level change, or as evidence that the signals are in some ways redundant with each other. Here, we compare a number of proxies representing the three main aspects of sampling, (1) sedimentary rock volume, (2) rock accessibility and (3) worker effort, with palaeodiversity in a geographically and stratigraphically constrained data set, the marine Lower Jurassic outcrop of the Dorset and East Devon Coast. We find that the proxies for rock volume and accessibility do not correlate well with the other sampling proxies, nor with apparent diversity, suggesting that the total amount of sedimentary rock preserved does not influence apparent diversity at a local scale, that is, the rock record at outcrop has been sampled efficiently. However, we do find some correlations between apparent diversity and proxies for worker effort. The fact that the proxies do not correlate significantly with each other suggests that none can be regarded as an all‐encompassing sampling proxy that covers all aspects of bias. Further, the presence of some correlations between sampling proxies and diversity most probably indicates the bonanza effect, as palaeontologists have preferentially sampled the richest rock units.     

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia

ABSTRACT: BACKGROUND: The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. RESULTS: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia connection, and later became extinct in North America. They only began substantive diversification during the Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. CONCLUSIONS: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.