The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Climate and the evolution of annual/perennial life-histories in Nemesia (Scrophulariaceae)

The Cape Floristic Region and the Succulent Karoo in southwestern Africa are both noted for their plant species richness and high levels of endemism. The southwestern tip of Africa is one of the world's five Mediterranean-type climate regions. The biodiversity in the Cape Floristic Region and Succulent Karoo is thought to be at least partly due to changes to the climate of these regions that have occurred since the middle Miocene. Annual species are usually a significant proportion of local flora in Mediterranean-type climate regions. Previous studies of species radiations in the Cape Floristic Region have concentrated on genera that predominantly contain perennial species. Nemesia (Scrophulariaceae) comprises c. 65 species of annual and perennial herbs and sub-shrubs that are native to southern and tropical Africa. Annuals make up a significant proportion (~75%) of Nemesia species. We have reconstructed a phylogeny of 23 Nemesia species using nucleotide sequences of the ITS, ETS and trnL-spacer regions. Species were grouped into five clades, two composed of annual species, one that contained two annual and one perennial species, one that contained one annual and two perennial species, and one that was predominantly composed of perennial species. Phylogenetic dating of the ITS + ETS based phylogenetic tree using penalised likelihood suggested the genus evolved during the Miocene, and that the majority of extant Nemesia species studied radiated during the Pliocene. Ancestral state reconstruction supports at least three separate origins of the annual habit from plants with a perennial life history. One origin can be traced to the late Miocene while the other two transitions occurred more recently during the Pliocene. The transition from perennial to annual life-histories in Nemesia may have been a response to climate change.     

Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes

Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (β-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose (Herpestes auropunctatus), the Indian gray mongoose (Herpestes edwardsii) and the Javan mongoose (Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.     

Marine incursions,cryptic species and ecological diversification in Amazonia: the biogeographic history of the croaker genus Plagioscion (Sciaenidae)

Aim We propose a phylogenetic hypothesis for the marine‐derived sciaenid genus Plagioscion in the context of geomorphology and adaptation to freshwaters of South America, and assess the extent to which contemporary freshwater hydrochemical gradients influence diversification within a widely distributed Plagioscion species, Plagioscion squamosissimus. Location Amazon Basin and South America. Methods Using nuclear and mitochondrial DNA sequence data, phylogenetic analyses were conducted on the five nominal Plagioscion species, together with representatives from Pachyurus and Pachypops, using character and model‐based methods. Genealogical relationships and population genetic structure of 152 P. squamosissimus specimens sampled from the five major rivers and three hydrochemical settings/‘colours’ (i.e. white, black and clear water) of the Amazon Basin were assessed. Results Phylogenetic analyses support the monophyly of Plagioscion in South America and identify two putative cryptic species of Plagioscion. Divergence estimates suggest that the Plagioscion ancestor invaded South America via a northern route during the late Oligocene to early Miocene. Within P. squamosissimus a strong association of haplotype and water colour was observed, together with significant population structure detected between water colours. Main conclusions Our analyses of Plagioscion are consistent with a biogeographic scenario of early Miocene marine incursions into South America. Based on our phylogenetic results, the fossil record, geomorphological history and distributional data of extant Plagioscion species, we propose that marine incursions into western Venezuela between the late Oligocene and early Miocene were responsible for the adaptation to freshwaters in Plagioscion species. Following the termination of the marine incursions during the late Miocene and the establishment of the modern Amazon River, Plagioscion experienced a rapid diversification. Plagioscion squamosissimus arose during that time. The formation of the Amazon River probably facilitated population and range expansions for this species. Further, the large‐scale hydrochemical gradients within the Amazon Basin appear to be acting as ecological barriers maintaining population discontinuities in P. squamosissimus even in the face of gene flow. Our results highlight the importance of divergent natural selection through time in the generation and maintenance of sciaenid diversity in Amazonia.     

Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae)

We have assessed for the first time the phylogenetic relationships and biogeographic history of the crabs of the genus Maja that inhabit European coasts: M. brachydactyla, M. crispata, M. goltziana and M. squinado. Using mitochondrial markers, we have recovered a well-resolved phylogenetic tree that supports a single origin for the European species, most likely from an Indo-West Pacific ancestor during the Early Miocene. In this phylogeny, M. goltziana appears as the basal European species, with a sister lineage bifurcating into an Eastern Atlantic (M. brachydactyla) and a Mediterranean (M. crispata and M. squinado) clade. We propose the Tethyan Seaway as the initial colonization route, although an entrance through South Africa cannot be discounted. The Eastern Atlantic/Mediterranean split seems to predate the Messinian salinity crisis, which, in turn, could have promoted the recent divergence within the Mediterranean. In addition, Pleistocene glaciations could explain the current diversity in the Eastern Atlantic Ocean, where a unique mitochondrial lineage is found. According to this, the genetic profile of South African crabs appears to belong to M. brachydactyla, questioning the validity of the putative species M. capensis.     

Molecular and morphological evidence for a Pleistocene radiation of laminate‐toothed rats (Otomys: Rodentia) across a volcanic archipelago in equatorial Africa

West African Mountains of the Cameroon Volcanic Line harbour two montane‐endemic species of laminated‐toothed rats (Otomys), which represent the most westerly occurrence of the genus. We explore here through mtDNA sequencing and cranial morphometrics the taxonomic status and phylogenetic relationships of O. burtoni (Mt Cameroon) and O. occidentalis (Mts Oku and Gotel). We conclude that both species are valid and can be discriminated by molecular data, as well as quantitative and qualitative cranial characters. From molecular data, O. occidentalis and O. burtoni are closest neighbours (p‐distance = 7.5–8.5%) and weakly associated sister species (suggesting a single West African radiation) and both are sister clades to a well supported clade of central, East and northeast African members of the O. typus s.l. and O. tropicalis s.l. species complexes from mountain ranges comprising the East African ‘Montane Circle’ and Ethiopian Highlands. Re‐evaluation of the evolutionary origins of the allopatric Otomys populations in equatorial Africa is undertaken in light of fossil evidence of a southern African origin of the genus. We can conclude that Otomys reached the Cameroon Volcanic Line via corridors of temperate grasslands during the Late Pliocene. Our data support the hypothesis that, following major peripatric speciation events at around 2.3 to 2.03 Ma (from East Africa into West and North Africa respectively), further speciation occurred across neighbouring mountain ranges in West, Central‐East and North‐East Africa. Estimated molecular dates of speciation events in Otomys reveal close congruence with well‐constrained geochronological estimates, pertinently the uplift of the Albertine Rift in the Early Pleistocene. These regional analyses reveal how peripatric speciation events established narrow‐range endemics of Otomys on principal stratovolcanoes across the East African plateau and Cameroon. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 320–344.     

Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes

American diploid cottons (Gossypium L., subgenus Houzingenia Fryxell) form a monophyletic group of 13 species distributed mainly in western Mexico, extending into Arizona, Baja California, and with one disjunct species each in the Galapagos Islands and Peru. Prior phylogenetic analyses based on an alcohol dehydrogenase gene (AdhA) and nuclear ribosomal DNA indicated the need for additional data from other molecular markers to resolve phylogenetic relationships within this subgenus. Toward this end, we sequenced three nuclear genes, the anonymous locus A1341, an alcohol dehydrogenase gene (AdhC), and a cellulose synthase gene (CesA1b). Independent and combined analyses resolved clades that are congruent with current taxonomy and previous phylogenies. Our analyses diagnose at least two long distance dispersal events from the Mexican mainland to Baja California, following a rapid radiation of the primary lineages early in the diversification of the subgenus. Molecular data support the proposed recognition of a new species closely related to Gossypium laxum that was recently collected in Mexico.     

Evolution of the African slippery frogs (Anura: Conraua), including the world’s largest living frog

Although Conraua goliath is well known as the largest living frog species, the diversity and evolution of the genus Conraua across sub-Saharan Africa remain poorly understood. We present multilocus phylogenetic analyses of the six currently recognized species that provide insights into divergence times, biogeography, body size evolution and undescribed species. An analysis of divergence times demonstrates that crown-group Conraua arose some time during the latest Oligocene to mid-Miocene followed by divergence into major lineages in the mid-Miocene that may reflect the fragmentation of widespread tropical forests in Africa that began at this time. We find three pairs of sister species, C. crassipes + C. beccarii, C. alleni + C. derooi and C. goliath + C. robusta, each of which diverged during the Miocene. These relationships reject phylogenetic hypotheses based solely on biogeography as the geographically peripheral C. beccarii from north-eastern Africa is nested within western African species and the Central African species do not form a clade. Our species delimitation analyses provide support for undescribed species in C. alleni, C. beccarii and C. derooi, and possibly C. crassipes, suggesting that the current taxonomy substantially underestimates species diversity. There is no clear directional trend of either increasing or decreasing body size in Conraua and the three largest species do not form a clade. With a robust phylogenetic hypothesis in hand, further field-based studies are needed to understand the evolution of morphology and life history in this charismatic African anuran clade.     

Freshwater gomphonemoid diatom phylogeny: preliminary results

A cladistic analysis of eleven freshwater gomphonemoid diatom taxa yielded three equally most parsimonious cladograms. The three cladograms suggest Gomphoneis Cleve is non-monophyletic as originally and recently circumscribed. Gomphoneis elegans and G. transsilvanica (Pant.) Krammer are more closely related to Gomphopleura Reichelt ex Tempère than to other members of the genus. Gomphoneis geitleri Kociolek & Stoermer appears to represent a monotypic lineage. Among the taxa with differentiated apical pore fields Gomphonema kaznakowi Mereschkowsky appears to be primitively astigmate.The three cladograms vary with regard to systematic affinities among the Gomphoneis herculeana (Ehrenberg) Cleve group, Miocene gomphonemoid species from Idaho (USA), gomphonemoid taxa from East Africa and Gomphonema sensu stricto. Despite variability in number of puncta rows per stria and presence of an axial plate in the Miocene species from North America, inclusion of these taxa in the analysis provided better resolution of relationships than if they were excluded.     

Molecular phylogeny of the blind cavefish <Emphasis Type="Italic">Phreatichthys andruzzii</Emphasis> and <Emphasis Type="Italic">Garra barreimiae</Emphasis> within the family Cyprinidae

The phylogenetic relationships of two cavefish, Phreatichthys andruzzii and Garra barreimiae, belonging to the family Cyprinidae, were investigated by sequencing the mitochondrial cytochrome b gene. These cavefish species are native to Somalia (eastern Africa) and Oman (southeastern Arabian peninsula), respectively, and so far no molecular support to their taxonomy and phylogenetic position was ever provided. The analysis of cytochrome b sequences showed that the species are monophyletic taxa, closely related to each other and to other species of the genus Garra. Molecular clock calculations allowed to date the origin of these hypogaean species back to the Plio-Pleistocene and support the hypothesis that African cyprinids originated from Miocenic immigrations of Asian ancestors.     

Biogeographical origins and diversification of the exoneurine allodapine bees of Australia (Hymenoptera,Apidae)

Aim Early diversification of allodapine bees occurred in Africa c. 50 Ma. They are most abundant in sub‐Saharan Africa and Australia, and one of the oldest phylogenetic divergences in the tribe involves a split between an African + Malagasy clade and an Australian clade. The historical biogeographical scenario for this has been highly problematic, entailing an Eocene dispersal from Africa to Australia, followed by an unresolved, and apparently rapid, set of bifurcations leading to the Australian ‘exoneurine’ genera. Here we use an expanded taxon set of Australian species to explore the timing and historical biogeography of the exoneurine radiation. Location Australia, Africa, Madagascar. Methods One nuclear gene (F2 copy of elongation factor 1α) and two mitochondrial genes (cytochrome c oxidase subunit I and cytochrome b) were sequenced for 33 Australian exoneurine species from all five genera found on the continent, as well as for an additional 37 species from all non‐parasitic genera in the remainder of the tribe. We used Bayesian inference analyses to study phylogenetic topology and penalized likelihood analyses to infer key dates of divergence within the tribe. We also used lineage‐through‐time (LTT) analyses and Bayesian analyses to explore the tempo of radiations and biogeographical history of the exoneurines. Results Results from the phylogenetic analyses were congruent with previous studies, indicating a single colonization event c. 34 Ma, too late for Gondwanan vicariance models, and too early for a Laurasian dispersal route. In contrast to earlier studies, we show that this colonization event did not result in an ancient rapid radiation. However, LTT patterns indicated a rapid radiation of the temperate‐adapted genera Exoneura and Brevineura, but not of the xeric‐adapted genus Exoneurella, from 10 to 6 Ma. Main conclusions Our results indicate a trans‐oceanic dispersal event from Africa to Australia, most likely via Antarctica, with an accelerated diversification of temperate‐adapted lineages during the major Late Miocene event referred to as the ‘Hill Gap’. This is the first study to link radiations in Australian bee faunal elements to changing climate, and differs from many other plant and insect phylogenetic studies by showing increased radiation of temperate clades, rather than xeric clades, with increasing aridification of Australia.     

Species delimitation in the Andean grasshopper genus Orotettix Ronderos & Carbonell (Orthoptera: Melanoplinae): an integrative approach combining morphological,molecular and biogeographical data

The reciprocal illumination nature of integrative taxonomy through hypothesis testing, corroboration and revision is a powerful tool for species delimitation as more than one source has to support the hypothesis of a new species. In this study, we applied an integrative taxonomy approach combining molecular and morphological data sets with distributional patterns to examine the level of differentiation between and within the grasshopper Orotettix species. Orotettix was described based on five valid species distributed in the Andes of Peru. In our study, initially a molecular‐based hypothesis was postulated and tested against morphological data and geographical patterns of distribution. Results from molecular and morphological analyses showed agreement among the species delimitation in Orotettix, and were also consistent with the geographical distribution. The analyses allowed us to delimit five new species for the genus ( O. lunatus sp. nov. , O . astreptos sp. nov. , O. colcaensis sp. nov. , O . paucartambensis sp. nov. and O . dichrous sp. nov. ) from the Eastern and Western Cordilleras of Peru. We also provide critical knowledge on the phylogenetic relationships and distribution of the genus and conduct a revision of Orotettix. © 2015 The Linnean Society of London     

Relationships of the MadagascarBignoniaceae: A striking case of convergent evolution

Most MadagascarBignoniaceae have indehiscent fruits and have been assigned to the tribeCrescentieae. As thus constituted, theCrescentieae are remarkably disjunct between Central America (and the West Indies) and Madagascar with a single monotypic genus also on continental Africa. This paper analyzes the evolutionary relationships of the MadagascarCrescentieae and concludes that they are descended from a different ancestral stock than the New WorldCrescentieae. A revised tribal taxonomy is proposed to reflect phylogenetic relationships withCrescentieae restricted to the neotropic species andColeeae resurrected for the indehiscent-fruited Madagascar species.     

Phylogeny of African fruit bats (Chiroptera,Pteropodidae) based on complete mitochondrial genomes

Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased frequency of guanine to adenine transitions is detected in the mtDNA genomes of Macroglossus sobrinus and all species of Casinycteris and Scotonycteris. Our phylogenetic and molecular dating analyses based on 126 taxa and 15,448 characters indicate a low signal for deep relationships within the family, suggesting a rapid diversification during the Late Oligocene period of “warming.” Within the subfamily Rousettinae, most nodes are highly supported by our different analyses (all nucleotide sites, SuperTRI analyses of a sliding window, transversions only, coding genes only, and amino acid sequences). The results indicate the existence of four tribes: Rousettini—distributed from Africa through Mediterranean region and South Asia to South-East Asia; Eonycterini—found in Asia; and Epomophorini and Scotonycterini—restricted to sub-Saharan Africa. Although most interspecies relationships are highly supported, three parts of the Rousettinae mitochondrial tree are still unresolved, suggesting rapid diversification: (a) among the three subtribes Epomophorina (Epomophorus sensu lato, i.e., including Micropteropus, Epomops, Hypsignathus, Nanonycteris), Plerotina (Plerotes), and Myonycterina (Myonycteris, Megaloglossus) in the Late Miocene; (b) among Epomops, Hypsignathus, and other species of Epomophorina at the Pliocene–Pleistocene boundary; and (c) among Myonycteris species in the Early Pleistocene. Within the Epomophorini, Stenonycteris lanosus emerged first, suggesting that lingual echolocation may have appeared in the common ancestor of Epomophorini and Rousettini. Our analyses suggest that multiple events of mtDNA introgression occurred within the Epomophorus species complex during the Pleistocene.     

Multiple in-to-Africa dispersals of labeonin fishes (Teleostei: Cyprinidae) revealed by molecular phylogenetic analysis

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (~23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (~ 20 MYA) and Late Miocene (~9 MYA) and serve as examples counter to out-of-Africa dispersal.     

Systematics and evolution of the Pan‐Alcidae (Aves,Charadriiformes)

Puffins, auks and their allies in the wing‐propelled diving seabird clade Pan‐Alcidae (Charadriiformes) have been proposed to be key pelagic indicators of faunal shifts in Northern Hemisphere oceans. However, most previous phylogenetic analyses of the clade have focused only on the 23 extant alcid species. Here we undertake a combined phylogenetic analysis of all previously published molecular sequence data (～ 12 kb) and morphological data (n = 353 characters) with dense species level sampling that also includes 28 extinct taxa. We present a new estimate of the patterns of diversification in the clade based on divergence time estimates that include a previously vetted set of twelve fossil calibrations. The resultant time trees are also used in the evaluation of previously hypothesized paleoclimatic drivers of pan‐alcid evolution. Our divergence dating results estimate the split of Alcidae from its sister taxon Stercorariidae during the late Eocene (～ 35 Ma), an evolutionary hypothesis for clade origination that agrees with the fossil record and that does not require the inference of extensive ghost lineages. The extant dovekie Alle alle is identified as the sole extant member of a clade including four extinct Miocene species. Furthermore, whereas an Uria + Alle clade has been previously recovered from molecular analyses, the extinct diversity of closely related Miocepphus species yields morphological support for this clade. Our results suggest that extant alcid diversity is a function of Miocene diversification and differential extinction at the Pliocene–Pleistocene boundary. The relative timing of the Middle Miocene climatic optimum and the Pliocene–Pleistocene climatic transition and major diversification and extinction events in Pan‐Alcidae, respectively, are consistent with a potential link between major paleoclimatic events and pan‐alcid cladogenesis.     

Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)

Drosophila is the genus responsible for the birth of experimental genetics, but the taxonomy of drosophilids is difficult because of the overwhelming diversity of the group. In this study, we assembled sequences for 358 species (14 genera, eight subgenera, 57 species groups, and 65 subgroups) to generate a maximum‐likelihood topology and a Bayesian timescale. In addition to sampling an unprecedented diversity of Drosophila lineages, our analyses incorporated a geographical perspective because of the high levels of endemism. In our topology, Drosophila funebris (Fabricius, 1787) (the type species of Drosophila) is tightly clustered with the pinicola subgroup in a North American clade within subgenus Drosophila. The type species of other drosophilid genera fall within the Drosophila radiation, presenting interesting prospects for the phylogenetic taxonomy of the group. Our timescale suggests that a few drosophilid lineages survived the Cretaceous–Palaeogene (K‐Pg) extinction. The drosophilid diversification began during the Palaeocene in Eurasia, but peaked during the Miocene, an epoch of drastic climatic changes. The most recent common ancestor of the clades corresponding to subgenera Sophophora and Drosophila lived approximately 56 Mya. Additionally, Hawaiian drosophilids diverged from an East Asian lineage approximately 26 Mya, which is similar to the age of the oldest emerging atoll in the Hawaiian–Emperor Chain. Interestingly, the time estimates for major geographical splits (New World versus Asia and Africa versus Asia) were highly similar for independent lineages. These results suggest that vicariance played a significant role in the radiation of fruit flies. © 2013 The Linnean Society of London