Early diversification trend and Asian origin for extent bat lineages

Bats are a unique mammalian group, which belong to one of the largest and most diverse mammalian radiations, but their early diversification is still poorly understood, and conflicting hypotheses have emerged regarding their biogeographic history. Understanding their diversification is crucial for untangling the enigmatic evolutionary history of bats. In this study, we elucidated the rate of diversification and the biogeographic history of extant bat lineages using genus‐level chronograms. The results suggest that a rapid adaptive radiation persisted from the emergence of crown bats until the Early Eocene Climatic Optimum, whereas there was a major deceleration in diversification around 35–49 Ma. There was a positive association between changes in the palaeotemperature and the net diversification rate until 35 Ma, which suggests that the palaeotemperature may have played an important role in the regulation of ecological opportunities. By contrast, there were unexpectedly higher diversification rates around 25–35 Ma during a period characterized by intense and long‐lasting global cooling, which implies that intrinsic innovations or adaptations may have released some lineages from the intense selective pressures associated with these severe conditions. Our reconstruction of the ancestral distribution suggests an Asian origin for bats, thereby indicating that the current panglobal but disjunct distribution pattern of extant bats may be related to events involving seriate cross‐continental dispersal and local extinction, as well as the influence of geological events and the expansion and contraction of megathermal rainforests during the Tertiary.     

Inference of higher-order relationships in the cycads from a large chloroplast data set

Theria includes Eutheria and its sister taxon Metatheria. Placentalia includes extant eutherians plus their most recent common ancestor. The oldest eutherian is from 125mya (million years ago). Molecular studies place this origin at about 130-185mya. Older dates cannot be refuted based on fossil evidence as earliest eutherian remains are scarce. Earliest superordinal clades (hence Placentalia) range from 64-104mya (median 84mya) based on molecules, similar to 85-90mya based on fossils. Superordinal clades Archonta, Ferungulata, Glires, and Paenungulata based on fossils are similar to molecularly based clades, except Afrotheria was not predicted by fossils. Both fossils and molecules recognize 16 of 18 extant placental orders. Fossils place the origins of orders around 65mya as do some molecular studies, but others suggest ordinal diversification as old as 100mya. Fossil evidence supports a Laurasian origin for Eutheria (and Metatheria) and Placentalia, although some molecular studies suggest a Gondwanan origin for both taxa.     

Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on noncoding nuclear and chloroplast DNA data

To examine relationships and test previous sectional delimitations within Fuchsia, this study used parsimony and maximum likelihood analyses with nuclear ITS and chloroplast trnL-F and rpl16 sequence data for 37 taxa representing all sections of Fuchsia and four outgroup taxa. Results support previous sectional delimitations, except for F. verrucosa, which is related to a Central American clade rather than to section Fuchsia and is described here as a new section Verrucosa. The basal relationships within Fuchsia are poorly resolved, suggesting an initial rapid diversification of the genus. Among the species sampled, there is strong support for a single South Pacific lineage, a southern South American/southern Brazilian lineage, a tropical Andean lineage, and one or two Central American and Mexican lineages. There is no clear support for an austral origin of the genus, as previously proposed, which is more consistent with Fuchsia's sister group relationship with the boreal Circaea. An ultrametric molecular clock analysis (all minimal dates) places the split between Fuchsia and Circaea at 41 million years ago (mya), with the diversification of the modern-day lineages of Fuchsia beginning at 31 mya. The South Pacific Fuchsia lineage branches off around 30 mya, consistent with fossil records from Australia and New Zealand. The large Andean section Fuchsia began to diversify around 22 mya, preceded by the divergence of the Caribbean F. triphylla at 25 mya. The Brazilian members of section Quelusia separated from the southern Andean F. magellanica around 13 mya, and the ancestor of the Tahitian F. cyrtandroides split off from the New Zealand species of section Skinnera approximately 8 mya.     

Evolution of the angiosperms: calibrating the family tree.

Growing evidence of morphological diversity in angiosperm flowers, seeds and pollen from the mid Cretaceous and the presence of derived lineages from increasingly older geological deposits both imply that the timing of early angiosperm cladogenesis is older than fossil-based estimates have indicated. An alternative to fossils for calibrating the phylogeny comes from divergence in DNA sequence data. Here, angiosperm divergence times are estimated using non-parametric rate smoothing and a three-gene dataset covering ca. 75% of all angiosperm families recognized in recent classifications. The results provide an initial hypothesis of angiosperm diversification times. Using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is performed. The origin of the crown group of extant angiosperms is indicated to be Early to Middle Jurassic (179-158 Myr), and the origin of eudicots is resolved as Late Jurassic to mid Cretaceous (147-131 Myr). Both estimates, despite a conservative calibration point, are older than current fossil-based estimates.     

Radiation and functional diversification of alpha keratins during early vertebrate evolution

The conquest of land was arguably one of the most fundamental ecological transitions in vertebrates and entailed significant changes in skin structure and appendages to cope with the new environment. In extant tetrapods, the rigidity of the integument is largely created by type I and type II keratins, which are structural proteins essential in forming a strong cytoplasmic network. It is expected that such proteins have undergone fundamental changes in both stem and crown tetrapods. Here, we integrate genomic, phylogenetic, and expression data in a comprehensive study on the early evolution and functional diversification of tetrapod keratins. Our analyses reveal that all type I and type II tetrapod keratins evolved from only two genes that were present in the ancestor of extant vertebrates. Subsequently, the water-to-land transition in the stem lineage of tetrapods was associated with a major radiation and functional diversification of keratin genes. These duplications acquired functions that serve rigidity in integumental hard structures and were the prime for subsequent independent keratin diversification in tetrapod lineages.     

Accelerated evolution of early angiosperms: Evidence from ranunculalean phylogeny by integrating living and fossil data

The new discovery of angiosperm remains in the Jehol Biota of northeastern China contributes to our understanding of the origin and early evolution of flowering plants. The earliest eudicot genus with reproductive organs, Leefructus, was recently documented from the Lower Cretaceous Yixian Formation at 125.8–123.0 Ma, and was reconsidered to be close to the extant family Ranunculaceae based on gross morphology. However, this hypothesis has not been tested using a cladistic approach. To determine the possible allies of Leefructus within extant eudicots, we constructed a 66 morphological data matrix. Molecular and morphological analyses of extant Ranunculales combined with the fossil suggest that it has an affinity with the Ranunculaceae. The earliest fossil record of the eudicots is 127–125 Ma based on tricolpate pollen grains. Thus, we suggest a hypothesis that the basal eudicots might have experienced an accelerated evolution and diversification during the latest Barremian and earliest Aptian, leading to the stem groups of at least six extant families or lineages, 10–15 Myr earlier than currently documented. Angiosperms have undergone multiple uneven pulses of radiation since their origin. Many key character innovations occurred in different stages that could have triggered those radiations in concert with various biotic and abiotic factors.     

Temporal patterns of diversification and microendemism in Eastern Highland endemic barcheek darters (Percidae: Etheostomatinae)

Eastern North America is the location of the world's most species-rich temperate freshwater fish fauna. Hypotheses regarding the geographic and temporal scale of teleost diversification in this region have not been broadly investigated using absolute divergence time estimates among the constituent lineages. This study used time-calibrated molecular phylogenies estimated from mitochondrial and nuclear genes to investigate the temporal and geographic signatures of diversification within barcheek darters, a clade of allopatrically distributed species endemic to the Eastern Highlands. Results from divergence time estimates using an uncorrelated lognormal model suggest that the barcheek darters are an ancient group with a crown node estimate of 16.3 mya, 95% highest posterior density (HPD): [12.4, 20.5], and the clade is characterized by substantial intraspecific divergence times within several species. In particular, the Caney Fork endemic Etheostoma basilare comprises five strongly supported and deeply divergent clades with a most recent common ancestor estimated at 8.0 mya, 95% HPD: [5.6, 10.7]. These results are concordant with the hypothesis that geologically stable areas of eastern North America have facilitated both the generation and preservation of lineages across a substantial breadth of evolutionary time, and that allopatric speciation in darters has occurred at much smaller spatial scales than previously realized.     

Molecular phylogeny and biogeography of Linanthus (Polemoniaceae)

To better understand the evolutionary history of Linanthus (Polemoniaceae) and its relatives, molecular phylogenies based on DNA sequence data from the internal transcribed spacer (ITS) region of nrDNA and the chloroplast gene matK were estimated using several methods. Our data suggest two separate and well-supported lineages of Linanthus in close association with two other genera-Leptodactylon and Phlox. These results agree with previous molecular systematic work on the Polemoniaceae, but do not support the traditional classification of the genus as a natural group, nor do they support the sectional classification within the genus. With a distribution centered primarily in western North America and a high degree of endemism in the California Floristic Province, it has been suggested by Raven and Axelrod that the origin and diversification of Linanthus and its relatives were tied to the development of a summer-dry climate in western North America, which began around 13-15 million years ago (mya). Increased drying during the Pliocene (1.2-5 mya) has also been hypothesized by Axelrod to have led to an increase in plant speciation in California and adjacent areas. Divergence times within the Linanthus lineages were estimated from the ITS and matK gene trees. A log-likelihood ratio test could not reject clock-like evolution for the matK data; however, the clock was strongly rejected for the ITS data set. Although ITS molecular evolution was not clock-like, the estimated times of divergence were similar to those of the matK data set. Within both lineages of Linanthus there seems to have been considerable diversification that has occurred since the Pliocene.     

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.     

Cladistic Analysis of A Problematic Ammonite Group: the Hamitidae (Cretaceous, Albian–turonian) and Proposals for New Cladistic Terms

The Hamitidae are a family of mid–Cretaceous heteromorph ammonites including lineages leading to four other families. Problems are outlined in trying to describe the phylogeny of completely extinct groups such as these heteromorph ammonites using the existing cladistic terminology, which is largely concerned with extant taxa and their ancestors. To solve these problems, two new terms are proposed: †crown groups and †stem groups, which are equivalent to crown and stem groups in terms of the evolutionary history of a clade, but are not defined on the basis of extant taxa. Instead they are defined by the topology of the phylogenetic tree, the †crown group being a clade defined by synapomorphies but which gave rise to no descendants. A †stem group is a branch of a phylogenetic tree which comprises the immediate sister groups of a given †crown group but is not itself a clade. Examples of these terms are described here with reference to the phylogeny of the Hamitidae and their descendants. The Hamitidae are paraphyletic and form †stem groups to a number of †crown groups, namely the Anisoceratidae, Baculitidae, Scaphitidae, and Turrilitidae. The definitions of the genera and subgenera are refined with respect to the type species and the clades within which they occur, and four new genera are described: Eohamites , Helicohamites , Sziveshamites , and Planohamites .     

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.     

Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants

Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species‐rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage‐wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.     

Molecular data from 27 proteins do not support a Precambrian origin of land plants

Heckman et al. (Science 293: 1129-1133) used sequences obtained from GenBank to infer divergence times in fungi and green plants. They estimated that the crown group of land plants originated in the Precambrian, at 703 ± 45 mya, a date much older than dates implied by the fossils, which are no older than about 450 mya. This paper presents an analysis of an entirely different set of sequence data from 27 plastid protein-coding genes in 10 land plants and a green algal outgroup. It uses a calibration point closer to the origin of land plants and inference methods that do not assume a molecular clock. This leads to estimates ranging from 425 to 490 mya, which brackets the age suggested by the fossil record. Possible explanations for the differing conclusions in the two studies include differences in calibration points and use of single-copy plastid genes rather than nuclear gene families.     

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Prosimians (tarsiers and strepsirrhini) represent the basal lineages in primates and have a close bearing on the origin of primates. Although major lineages among anthropoidea (humans, apes and monkeys) are well represented by complete mitochondrial DNA (mtDNA) sequence data, only one complete mtDNA sequence from a representative of each of the infraorders in prosimians has been described until quite recently, and therefore we newly determined complete mtDNA sequences from 5 lemurs, 4 lorises, one tarsier and one platyrrhini. These sequences were provided to phylogenetic analyses in combination with the sequences from the 15 primates species reported to the database. The position of tarsiers among primates could not be resolved by the maximum likelihood (ML) and neighbor-joining (NJ) analyses with several data sets. As to the position of tarsiers, any of the three alternative topologies (monophyly of haplorhini, monophyly of prosimians, and tarsiers being basal in primates) was not rejected at the significance level of 5%, neither at the nucleotide nor at the amino acid level. In addition, the significant variations of C and T compositions were observed across primates species. Furthermore, we used AGY data sets for phylogenetic analyses in order to remove the effect of different C/T composition bias across species. The analyses of AGY data sets provided a medium support for the monophyly of haplorhini, which might have been screened by the variation in base composition of mtDNA across species. To estimates the speciation dates within primates, we analyzed the amino acid sequences of mt-proteins with a Bayesian method of Thorne and Kishino. Divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for lorisiformes, 55.3 mya for lemuriformes, 64.5 mya for strepsirrhini, 70.1 mya for haplorhini and 76.0 mya for primates. Furthermore, we reexamined the biogeographic scenarios which have been proposed for the origin of strepsirrhini (lemuriformes and lorisiformes) and for the dispersal of the lemuriformes and lorisiformes.     

Eocene Diversification of Crown Group Rails (Aves: Gruiformes: Rallidae)

Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.     

Bees diversified in the age of eudicots

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.     

Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated.     

The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals

Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and anthophagy. The ingroup-based fossil calibration of the tree widely confirmed a Jurassic origin of the Scarabaeoidea crown group. The crown groups of phytophagous lineages began to radiate first (Pleurostict scarabs: 108 Ma; Glaphyridae between 101 Ma), followed by the later diversification of coprophagous lineages (crown-group age Scarabaeinae: 76 Ma; Aphodiinae: 50 Ma). Pollen feeding arose even later, at maximally 62 Ma in the oldest anthophagous lineage. The clear time lag between the origins of herbivores and coprophages suggests an evolutionary path driven by the angiosperms that first favoured the herbivore fauna (mammals and insects) followed by the secondary radiation of the dung feeders. This finding makes it less likely that extant dung beetle lineages initially fed on dinosaur excrements, as often hypothesized.     

Molecular evidence for Gondwanan origins of multiple lineages within a diverse Australasian gecko radiation

Aim Gondwanan lineages are a prominent component of the Australian terrestrial biota. However, most squamate (lizard and snake) lineages in Australia appear to be derived from relatively recent dispersal from Asia (< 30 Ma) and in situ diversification, subsequent to the isolation of Australia from other Gondwanan landmasses. We test the hypothesis that the Australian radiation of diplodactyloid geckos (families Carphodactylidae, Diplodactylidae and Pygopodidae), in contrast to other endemic squamate groups, has a Gondwanan origin and comprises multiple lineages that originated before the separation of Australia from Antarctica. Location Australasia. Methods Bayesian (beast ) and penalized likelihood rate smoothing (PLRS) (r 8s ) molecular dating methods and two long nuclear DNA sequences (RAG‐1 and c‐mos) were used to estimate a timeframe for divergence events among 18 genera and 30 species of Australian diplodactyloids. Results At least five lineages of Australian diplodactyloid geckos are estimated to have originated > 34 Ma (pre‐Oligocene) and basal splits among the Australian diplodactyloids occurred c. 70 Ma. However, most extant generic and intergeneric diversity within diplodactyloid lineages appears to post‐date the late Oligocene (< 30 Ma). Main conclusions Basal divergences within the diplodactyloids significantly pre‐date the final break‐up of East Gondwana, indicating that the group is one of the most ancient extant endemic vertebrate radiations east of Wallace’s Line. At least five Australian lineages of diplodactyloid gecko are each as old or older than other well‐dated Australian squamate radiations (e.g. elapid snakes and agamids). The limbless Pygopodidae (morphologically the most aberrant living geckos) appears to have radiated before Australia was occupied by potential ecological analogues. However, in spite of the great age of the diplodactyloid radiation, most extant diversity appears to be of relatively recent origin, a pattern that is shared with other Australian squamate lineages.     

Understanding angiosperm diversification using small and large phylogenetic trees

How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the sample of species in GenBank is at least roughly proportional to the actual species diversity of different lineages, as appears to be the case for many major angiosperm lineages. Using both approaches, we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades. Based on our mega-phylogeny, the shifts in diversification appear to be distributed quite evenly throughout the angiosperms. Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation.