Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ～53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (～34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (～26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (～14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.     

British mammals in the Tertiary period

British Tertiary mammals are best represented in the Eocene and earliest Oligocene epochs. Additional occurrences are from the Miocene and Late Pliocene. The Eocene is marked by the occurrence of various extinct orders as well as the appearances of some of the earliest and must primitive artiodactyls and perissodactyls. The appearances in the Early Eocene and Early Oligocene represent major dispersal events, reflecting penecontemporaneous palaeogeographic changes. In the intervening timespan Britain was part of an European island, sharing its endemic terrestrial fauna. From the late Middle Eocene to earliest Oligocene, the British record is detailed enough to trace successive changes in the patterns of diversity and faunal turnover, which may relate to changing climate as well as to the dispersal events. It has been shown that changes in patterns of ecological diversity through the Eocene and earliest Oligocene match vegetational changes judged from plant fossils. They suggest a gradual transition from closed forest in the Early Eocene to a more open environment with reedmarsh and wooded patches by the end of the epoch.     

The explosive diversification of the diatom genus Chaetoceros across the Eocene/Oligocene and Oligocene/Miocene boundaries in the Norwegian Sea

Eocene to middle Miocene stratigraphic changes in species richness, abundance and valve size of Chaetoceros resting spores in the Norwegian Sea (DSDP Site 338) were investigated in order to understand past productivity and paleoenvironmental changes in upwelling regions. As a result, drastic resting spore events were recognized in a 6 myr interval across the Eocene/Oligocene boundary (EO Event), the Oligocene/Miocene boundary (OM Event) and in the early middle Miocene (emM Event). The EO Event was characterized by explosive diversification at both the morpho-generic and specific levels, an increase in abundance, and a decrease in valve size from the upper Eocene through the lowest Oligocene. The OM Event was defined by a two-fold increase in species richness. During the emM Event spore abundance decreased rapidly, and species richness and valve size decreased gradually. These changes may indicate changes in the nutrient supply, especially in upwelling regions. The increased species richness suggests a change from a stable water column with a constant nutrient supply in the Eocene to an unstable one with a sporadic nutrient supply by increased vertical mixing in the Oligocene, based on evaluation of the ecologic differences between dinoflagellate cysts and Chaetoceros resting spores. The role of main primary producer might have switched from dinoflagellates and/or nannoplankton in the Eocene to diatoms, especially Chaetoceros, in the Oligocene in the Norwegian Sea. Increased resting spore species richness during the OM Event may show that environmental changes such as global cooling and nutrient mixing led to a diversification of the spore producing genus Chaetoceros. The emM Event might have been affected by changes in paleoceanographic conditions, perhaps a decrease in nutrient supply. This study presents the first paleoceanographic analysis using not only the total resting spore abundance but also the abundances of individual species, and establishes the value of spore taxonomy and diatom analysis including spores.     

Historical biogeography, divergence times, and diversification patterns of bumble bees (Hymenoptera: Apidae: Bombus)

Bumble bees (Bombus) are a cold-adapted, largely alpine group that can elucidate patterns of Holarctic historical biogeography, particularly in comparison to the alpine plants with which they likely coevolved. A recently published molecular phylogeny of bumble bees provides uniquely comprehensive species sampling for exploring historical patterns of distribution and diversification. Using this phylogeny and detailed data on extant distributions, I reconstruct the historical distribution of bumble bees in a temporal framework, estimating divergence times using fossil data and molecular rates derived from the literature. The nearly comprehensive phylogeny allows assessment of the tempo of diversification within the bumble bees using lineage-through-time plots and diversification statistics, which have been performed with special consideration to confidence intervals. These analyses reveal movements of Bombus concordant with geographic and climatic events of the late Cenozoic. The initial diversification of extant bumble bee lineages was estimated at around 25 to 40 Ma, near the Eocene-Oligocene boundary 34 Ma, a period of dramatic global cooling. Dispersal-vicariance analysis (DIVA) predicted an Old World Bombus ancestor, with early diversification events largely restricted to the eastern Old World. The numerous intercontinental dispersal events occurred mostly in the direction of Old World to New World and North America to South America. Early movements from the Palearctic into the Nearctic most likely took place after 20 Ma and may have coincided with a period of Miocene cooling that gave rise to taiga habitat across Beringia. Subsequent dispersal between these regions is estimated to have occurred among boreal and tundra-adapted species mostly in the last 5 million years. Radiations are estimated in both Nearctic and Neotropical regions at approximately 6 to 8 Ma and after 3.5 Ma, concordant with the opening of land corridors between the continents.     

The Phylogeny and Biogeographic History of Ashes (Fraxinus,Oleaceae) Highlight the Roles of Migration and Vicariance in the Diversification of Temperate Trees

The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.     

Major Radiations in the Evolution of Caviid Rodents: Reconciling Fossils,Ghost Lineages,and Relaxed Molecular Clocks

Background

Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”).

Results

A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates.

Conclusions

The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.     

Acrobat ants go global - Origin, evolution and systematics of the genus Crematogaster (Hymenoptera: Formicidae)

This study unravels the evolution and biogeographic history of the globally distributed ant genus Crematogaster on the basis of a molecular phylogeny, reconstructed from five nuclear protein-coding genes and a total of 3384bp of sequence data. A particular emphasis is placed on the evolutionary history of these ants in the Malagasy region. Bayesian and likelihood analyses performed on a dataset of 124 Crematogaster ingroup taxa lend strong support for three deeply diverging phylogenetic lineages within the genus: the Orthocrema clade, the Global Crematogaster clade and the Australo-Asian Crematogaster clade. The 15 previous subgenera within Crematogaster are mostly not monophyletic. Divergence dating analyses and ancestral range reconstructions suggest that Crematogaster evolved in South-East Asia in the mid-Eocene (40-45ma). The three major lineages also originated in this region in the late Oligocene/early Miocene (～24-30ma). A first dispersal out of S-E Asia by an Orthocrema lineage is supported for 22-30ma to the Afrotropical region. Successive dispersal events out of S-E Asia began in the early, and continued throughout the late Miocene. The global distribution of Crematogaster was achieved by subsequent colonizations of all major biogeographic regions by the Orthocrema and the Global Crematogaster clade. Molecular dating estimates and ancestral range evolution are discussed in the light of palaeogeographic changes in the S-E Asian region and an evolving ocean circulation system throughout the Eocene, Oligocene and Miocene. Eight dispersal events to/from Madagascar by Crematogaster are supported, with most events occurring in the late Miocene to Pliocene (5.0-9.5ma). These results suggest that Crematogaster ants possess exceptional dispersal and colonization abilities, and emphasize the need for detailed investigations of traits that have contributed to the global evolutionary success of these ants.     

Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae)

Although the deserts of North America are of very recent origin, their characteristic arid-adapted endemic plant lineages have been suggested to be much older. Earlier researchers have hypothesized that the ancestors of many of these modern desert lineages first adapted to aridity in highly localized arid or semi-arid sites as early as the late Cretaceous or early Tertiary, and that these lineages subsequently spread and diversified as global climate became increasingly arid during the Cenozoic. No study has explicitly examined these hypotheses for any North American arid-adapted plant group. The current paper tests these hypotheses using the genus Tiquilia (Boraginaceae), a diverse North American desert plant group. A strongly supported phylogeny of the genus is estimated using combined sequence data from three chloroplast markers (matK, ndhF, and rps16) and two nuclear markers (ITS and waxy). Ages of divergence events within the genus are estimated using penalized likelihood and a molecular clock approach on the ndhF tree for Tiquilia and representative outgroups, including most of the major lineages of Boraginales. The dating analysis suggests that the stem lineage of Tiquilia split from its nearest extant relative in the Paleocene or Eocene ( approximately 59-48 Ma). This was followed by a relatively long period before the first divergence in the crown group near the Eocene/Oligocene boundary ( approximately 33-29 Ma), shortly after the greatest Cenozoic episode of rapid aridification. Divergence of seven major lineages of Tiquilia is dated to the early-to-mid Miocene ( approximately 23-13 Ma). Several major lineages show a marked increase in diversification concomitant with the onset of more widespread semi-arid and then arid conditions beginning in the late Miocene ( approximately 7 Ma). This sequence of divergence events in Tiquilia agrees well with earlier researchers' ideas concerning North American desert flora assembly.     

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)

Recent expeditions have revealed high levels of biodiversity in the tropical deep‐sea, yet little is known about the age or origin of this biodiversity, and large‐scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep‐sea gastropods (1) to test the hypothesis that deep‐water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep‐water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene–Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep‐sea habitats. Tectonic events that shaped diversification in reef‐associated taxa and deep‐water squat lobsters in central Indo‐West Pacific were also probably important in the evolution of solariellids during the Oligo‐Miocene.     

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.     

FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS,GENERIC DIVERSITY,AND TURNOVER RATES ARE DISCONNECTED

The magnitude and extent of global change during the Cenozoic is remarkable, yet the impacts of these global changes on the biodiversity and evolutionary dynamics of species diversification remain poorly understood. To investigate this question, we combine paleontological and neontological data for the angiosperm order Fagales, an ecologically important clade of about 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates for Fagales. Generic diversity evolved rapidly since the Late Cretaceous and peaked during the Eocene or Oligocene. Turnover rates were high during periods of extreme global climate change, but relatively low when the climate remained stable. Species richness accumulated gradually throughout the Cenozoic, possibly at an accelerated pace after the Middle Miocene. Species diversification occurred in new environments: Quercoids radiating in Oligocene subtropical seasonally arid habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula in Late Neogene holarctic habitats. These radiations were counterbalanced by regional extinctions in Late Neogene mesic warm‐temperate forests. Thus, the overall diversification at species level is linked to regional radiations of clades with appropriate ecologies exploiting newly available habitats.     

Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses

Lebedev, V.S., Bannikova, A.A., Pagès, M., Pisano, J., Michaux, J.R. & Shenbrot, G.I. (2012). Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses. —Zoologica Scripta, 42, 231–249. The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid‐dwelling jerboas (Dipodinae – three‐toed jerboas, Allactaginae – five‐toed jerboas, Cardiocraniinae – pygmy jerboas and Euchoreutinae – long‐eared jerboas), the other two are represented by more generalized quadrupedal taxa (Zapodinae – jumping mice and Sminthinae – birch mice). Despite considerable effort from morphologists, the taxonomy as well as the phylogeny of the Dipodoidea remains controversial. Strikingly, molecular approach has never been envisaged to investigate these questions. In this study, the phylogenetic relationships among the main dipodoid lineages were reconstructed for the first time using DNA sequence data from four nuclear genes (IRBP, GHR, BRCA1, RAG1). No evidence of conflict among genes was revealed. The same robustly supported tree topology was inferred from the concatenated alignment whatever the phylogenetic methods used (maximum parsimony, maximum‐likelihood and Bayesian phylogenetic methods). Sminthinae branches basally within the dipodoids followed by Zapodinae. Monophyletic Cardiocraniinae is sister to all other jerboas. Within the latter, the monophyly of both Dipodinae and Allactaginae is highly supported. The relationships between Dipodinae, Allactaginae and Euchoreutinae should be regarded as unresolved trichotomy. Morphological hypotheses were confronted to findings based on the presented molecular data. As a result, previously proposed sister group relationships between Euchoreutes and Sicista, Paradipus and Cardiocraniinae as well as the monophyly of Cardiocaniinae + Dipodinae were rejected. However, the latter association is consistently supported by most morphological analyses. The basis of the obvious conflict between genes and morphology remains unclear. Suggested modifications to the taxonomy of Dipodoidea imply recognition of three families: Sminthidae, Zapodidae and Dipodidae, the latter including Cardiocraniinae, Euchoreutinae, Allactaginae and Dipodinae as subfamilies.     

Deep-sea benthonic foraminiferal faunal turnover near the Eocene/Oligocene boundary

Eocene-Oligocene deep-sea benthonic foraminifera in D.S.D.P. Site 277 in the southwest Pacific have been analyzed to determine the benthonic foraminiferal response to the development of the psychrosphere near the Eocene/Oligocene boundary. Biostratigraphic ranges of 41 taxa show that 23 taxa are found throughout the Late Eocene to Early Oligocene sequence, while 18 taxa exhibit first or last occurrences. Comparison of the faunal changes in Site 277 with a benthonic foraminiferal oxygen isotope record shows that the development of the psychrosphere did not have a profound effect upon the benthonic foraminifera, and the overall faunal change preceding and subsequent to the bottom-water circulation event occurred gradually. The inferred water-mass event affected the relative abundance of one species, Epistominella umbonifera. The lack of major faunal changes at the Eocene/Oligocene boundary in Site 277 probably reflects either wide environmental tolerances of the benthonic foraminifera, or a bottom-water temperature change less than 3°C.Examination of previously published benthonic foraminiferal biostratigraphic data from D.S.D.P. Sites 167, 171, 357, 360, 363, and 400A, and deep-sea ostracode data from D.S.D.P. Leg 3 show faunal changes occurred during discrete intervals in the Middle Eocene-Early Oligocene. The faunal patterns from these data and from Site 277 show that the Eocene/Oligocene cooling event did not cause rapid, catastrophic changes of the benthonic faunas of the open ocean, although significant faunal changes are associated with the water mass event in Sites 167, 171 and 400A.The benthonic faunal changes in Middle Eocene-Early Oligocene time are consistent with the gradual decrease of inferred bottom-water temperatures, based on previously published oxygen isotopic data. The δ ¹⁸O Eocene/Oligocene enrichment of 0.76‰ is a major event in the Southern Ocean oxygen isotopic record, but is considerably less in magnitude than the 1.75-2.00‰ change that occurred gradually from mid-Early Eocene to the Eocene/Oligocene boundary. The benthonic foraminiferal and isotopic data indicate that bottom-water circulation may have developed during the Middle Eocene to Early Oligocene interval, with the 3°C bottom-water cooling near the Eocene/Oligocene boundary representing part of this development.     

Middle Eocene–late Oligocene climate variability: Calcareous nannofossil response at Kerguelen Plateau,Site 748

A major deterioration in global climate occurred through the Eocene–Oligocene time interval, characterized by long-term cooling in both terrestrial and marine environments. During this long-term cooling trend, however, recent studies have documented several short-lived warming and cooling phases. In order to further investigate high-latitude climate during these events, we developed a high-resolution calcareous nannofossil record from ODP Site 748 Hole B for the interval spanning the late middle Eocene to the late Oligocene (~ 42 to 26 Ma). The primary goals of this study were to construct a detailed biostratigraphic record and to use nannofossil assemblage variations to interpret short-term changes in surface-water temperature and nutrient conditions. The principal nannofossil assemblage variations are identified using a temperate-warm-water taxa index (Twwt), from which three warming and five cooling events are identified within the middle Eocene to the earliest Oligocene interval. Among these climatic trends, the cooling event at ~ 39 Ma (Cooling Event B) is recorded here for the first time. Variations in fine-fraction δ¹⁸O values at Site 748 are associated with changes in the Twwt index, supporting the idea that significant short-term variability in surface-water conditions occurred in the Kerguelen Plateau area during the middle and late Eocene. Furthermore, ODP Site 748 calcareous nannofossil paleoecology confirms the utility of these microfossils for biostratigraphic, paleoclimatic, and paleoceanographic reconstructions at Southern Ocean sites during the Paleogene.     

The oldest lamprophiid (Serpentes,Caenophidia) fossil from the late Oligocene Rukwa Rift Basin,Tanzania and the origins of African snake diversity

Extant snake faunas have their origins in the mid-Cenozoic, when colubroids replaced booid-grade snakes as the dominant species. The timing of this faunal changeover in North America and Europe based on fossils is thought to have occurred in the early Neogene, after a period of global cooling opened environments and made them suitable for more active predators. However, new fossils from the late Oligocene of Tanzania have revealed an early colubroid-dominated fauna in Africa suggesting a different pattern of faunal turnover there. Additionally, molecular divergence times suggest colubroid diversification began sometime in the Paleogene, although the exact timing and driving forces behind the diversification are not clear. Here we present the first fossil snake referred to the African clade Lamprophiinae, and the oldest fossil known of Lamprophiidae. As such, this specimen provides the only potential fossil calibration point for the African snake radiation represented by Lamprophiidae, and is the oldest snake referred to Elapoidea. A molecular clock analysis using this and other previously reported fossils as calibration points reveals colubroid diversification minimally occurred in the earliest Paleogene, although a Cretaceous origin cannot be excluded. The elapoid and colubrid lineages diverged during the period of global warming near the Paleocene-Eocene boundary, with both clades diversifying beginning in the early Eocene (proximate to the Early Eocene Climate Optimum) and continuing into the cooler Miocene. The majority of subclades diverge well before the appearance of colubroid dominance in the fossil record. These results suggest an earlier diversification of colubroids than generally previously thought, with hypothesized origins of these clades in Asia and Africa where the fossil record is relatively poorly known. Further work in these regions may provide new insights into the timing of, and environmental influences contributing to, the rise of colubroid snakes.     

Insights into the historical construction of species-rich Mesoamerican seasonally dry tropical forests: the diversification of Bursera (Burseraceae, Sapindales)

? Mesoamerican arid biomes epitomize neotropical rich and complex biodiversity. To document some of the macroevolutionary processes underlying the vast species richness of Mesoamerican seasonally dry tropical forests (SDTFs), and to evaluate specific predictions about the age, geographical structure and niche conservatism of SDTF-centered woody plant lineages, the diversification of Bursera is reconstructed. ? Using a nearly complete Bursera species-level phylogeny from nuclear and plastid genomic markers, we estimate divergence times, test for phylogenetic and temporal diversification heterogeneity, test for geographical structure, and reconstruct habitat shifts. ? Bursera became differentiated in the earliest Eocene, but diversified during independent early Miocene consecutive radiations that took place in SDTFs. The late Miocene average age of Bursera species, the presence of phylogenetic geographical structure, and its strong conservatism to SDTFs conform to expectations derived from South American SDTF-centered lineages. ? The diversification of Bursera suggests that Mesoamerican SDTF richness derives from high speciation from the Miocene onwards uncoupled from habitat shifts, during a period of enhanced aridity resulting mainly from global cooling and regional rain shadows.     

Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots

Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae and Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef-associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the recent IAA marine biodiversity hotspot.     

Main radiation events in Pan‐Octodontoidea (Rodentia,Caviomorpha)

Caviomorphs (South American hystricognaths) are recorded in the continent since the middle Eocene. The middle Eocene–early Oligocene is considered a key moment for their evolutionary history because by the early Oligocene they were differentiated into four superfamilies: Octodontoidea, Cavioidea, Chinchilloidea and Erethizontoidea. Due to their generalized dental patterns and abundance in the fossil record, Octodontoidea are interesting for analysing the origin and early history of caviomorphs. The phylogenetic relationships of the earliest octodontoids are studied herein. Results confirmed a basal caviomorph diversification in the middle Eocene (c. 45 Mya), with one lineage leading to Pan‐Octodontoidea, and another leading to Erethizontoidea, Cavioidea and Chinchilloidea, which is not in accordance with analyses based on molecular data. Three major radiations were identified: the first one (late Eocene?/early Oligocene?) occurred in low latitudes with the differentiation of Pan‐Octodontoidea and the earliest crown‐Octodontoidea. The second radiation (late Oligocene) was a large‐scale South American event; in the southernmost part of the continent it is recognized as the first Patagonian octodontoid radiation, which provided the characteristic high morphological disparity of the superfamily. The third radiation (late Miocene) is characterized by the replacement of ‘old’ by ‘modern’ octodontoids; the nature of this third event needs to be study in a broader taxonomic context. © 2015 The Linnean Society of London     

Mass turnover and recovery dynamics of a diverse Australian continental radiation

Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene‐Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australia's most diverse endemic radiations, pygopodoid geckos. We generated a time‐calibrated phylogeny (>90% taxon coverage) to test whether (i) asymmetrical pygopodoid tree shape may be the result of mass turnover deep in the group's history, and (ii) how Miocene aridification shaped trends in biome assemblages. We find evidence of mass turnover in pygopodoids following the isolation of the Australian continental plate ～30 million years ago, and in contrast, gradual aridification is linked to elevated speciation rates in the young arid zone. Surprisingly, our results suggest that invasion of arid habitats was not an evolutionary end point. Instead, arid Australia has acted as a source for diversity, with repeated outward dispersals having facilitated diversification of this group. This pattern contrasts trends in richness and distribution of other Australian vertebrates, illustrating the profound effects historical biome changes have on macroevolutionary patterns.     

Complex co-evolutionary relationships between cicadas and their symbionts

Previous evidence suggests that cicadas lacking Hodgkinia may harbour the yeast-like fungal symbionts (YLS). Here, we reinforce an earlier conclusion that the pathogenic ancestor of YLS independently infected different cicada lineages instead of the common ancestor of Cicadidae. Five independent replacement events in the loss of Hodgkinia/acquisition of YLS and seven other replacement events of YLS (from an Ophiocordyceps fungus to another Ophiocordyceps fungus) are hypothesised to have occurred within the sampled cicada taxa. The divergence time of YLS lineages was later than that of corresponding cicada lineages. The rapid shift of diversification rates of YLS and related cicada-parasitizing Ophiocordyceps began at approximately 32.94 Ma, and the diversification rate reached the highest value at approximately 24.82 Ma, which corresponds to the cooling climate changes at the Eocene–Oligocene boundary and the Oligocene–Miocene transition respectively. Combined with related acquisition/replacement events of YLS occurred during the cooling-climate periods, we hypothesise that the cooling-climate changes impacted the interactions between cicadas and related Ophiocordyceps, which coupled with the unusual life cycle and the differentiation of cicadas may finally led to the diversification of YLS in Cicadidae. Our results contribute to a better understanding of the evolutionary transition of YLS from entomopathogenic fungi in insects.