New adapiform primate of Old World affinities from the Devil's Graveyard Formation of Texas

Most adapiform primates from North America are members of an endemic radiation of notharctines. North American notharctines flourished during the Early and early Middle Eocene, with only two genera persisting into the late Middle Eocene. Here we describe a new genus of adapiform primate from the Devil’s Graveyard Formation of Texas. Mescalerolemur horneri, gen. et sp. nov., is known only from the late Middle Eocene (Uintan) Purple Bench locality. Phylogenetic analyses reveal that Mescalerolemur is more closely related to Eurasian and African adapiforms than to North American notharctines. In this respect, M. horneri is similar to its sister taxon Mahgarita stevensi from the late Duchesnean of the Devil’s Graveyard Formation. The presence of both genera in the Big Bend region of Texas after notharctines had become locally extinct provides further evidence of faunal interchange between North America and East Asia during the middle Eocene. The fact that Mescalerolemur and Mahgarita are both unknown outside of Texas also supports prior hypotheses that low-latitude faunal assemblages in North America demonstrate increased endemism by the late middle Eocene.     

Talar morphology of azibiids, strepsirhine-related primates from the Eocene of Algeria: phylogenetic affinities and locomotor adaptation

The HGL-50 locality, situated on the Glib Zegdou outlier in the Gour Lazib of Algeria (Hammada du Dra), is famous for having yielded several dental remains of primates dating from the late Early to the early Middle Eocene. These primates include Algeripithecus minutus, Azibius trerki and a new species of cf. Azibius (not described yet). Algeripithecus was widely acknowledged to be one of the oldest known anthropoids from Africa. However, very recent discoveries strongly suggest that Algeripithecus is closely related to Azibius and that both taxa are phylogenetically remote from the clade Anthropoidea. Algeripithecus and Azibius make up the family Azibiidae and appear as stem strepsirhines. Here we describe and analyse two ankle bones (tali) found in HGL-50. UM/HGL50-466 is a small left talus, which is appropriate in size to belong to A. trerki, while UM/HGL50-467 is a right talus, which is significantly larger and appropriate in size to belong to the new large species of cf. Azibius. Both tali exhibit a suite of features that resemble conditions primarily found in extinct and extant strepsirhine and adapiform primates; conditions that are consistent with the strepsirhine-like dentition characterizing azibiids. Functionally, these two tali indicate that Azibius species were engaged in a form of active arboreal quadrupedalism with some ability to climb and leap. Azibiids were rather small-bodied primates, approximating the size of some modern dwarf lemurs (Cheirogaleidae) and sportive lemurs (Lepilemuridae) from Madagascar. Given their small body-size and their talar morphology, living cheirogaleid lemurs, which are agile arboreal quadrupeds (with climbing, springing and branch running activities), might appear as good analogues for azibiids in terms of locomotor behaviour.     

A remarkable short-snouted horned dinosaur from the Late Cretaceous (late Campanian) of southern Laramidia

The fossil record of centrosaurine ceratopsids is largely restricted to the northern region of western North America (Alberta, Montana and Alaska). Exceptions consist of single taxa from Utah (Diabloceratops) and China (Sinoceratops), plus otherwise fragmentary remains from the southern Western Interior of North America. Here, we describe a remarkable new taxon, Nasutoceratops titusi n. gen. et sp., from the late Campanian Kaiparowits Formation of Utah, represented by multiple specimens, including a nearly complete skull and partial postcranial skeleton. Autapomorphies include an enlarged narial region, pneumatic nasal ornamentation, abbreviated snout and elongate, rostrolaterally directed supraorbital horncores. The subrectangular parietosquamosal frill is relatively unadorned and broadest in the mid-region. A phylogenetic analysis indicates that Nasutoceratops is the sister taxon to Avaceratops, and that a previously unknown subclade of centrosaurines branched off early in the group''s history and persisted for several million years during the late Campanian. As the first well-represented southern centrosaurine comparable in age to the bulk of northern forms, Nasutoceratops provides strong support for the provincialism hypothesis, which posits that Laramidia—the western landmass formed by inundation of the central region of North America by the Western Interior Seaway—hosted at least two coeval dinosaur communities for over a million years of late Campanian time.     

A new basal tapiromorph (Perissodactyla, Mammalia) from the middle Eocene of Myanmar

A new genus and species of tapiromorph, Skopaiolophus burmese nov. gen., nov. sp., is described from the middle Eocene Pondaung Formation in central Myanmar. This small form displays a striking selenolophodont morphology associated with a mixture of primitive “condylarthran” dental characters and derived tapiromorph features. Skopaiolophus is here tentatively referred to a group of Asian tapiromorphs unknown so far. The occurrence of such a form in Pondaung suggests that primitive tapiromorphs might have persisted in southeast Asia until the late middle Eocene while they became extinct elsewhere in both Eurasia and North America.     

A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera,Noctuidae, Oncocnemidinae)

A Triosteum-feeding species of Sympistis is described from eastern North America: Sympistis forbesi sp. n. Identity of the new species is most reliably determined from larval morphology and host plant association—both adult scaling and genitalic characters overlap with those of Sympisitis chionanthi, a Chionanthus and Fraxinus feeder.     

Ancient collagen reveals evolutionary history of the endemic South American ‘ungulates’

Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.     

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4–386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6–6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.     

Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an ‘extinct’ avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O''Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.     

Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions

Predicting species'' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host–pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host–pathogen coevolution.     

Reticulate evolution in North American black-fruited hawthorns (Crataegus section Douglasia; Rosaceae): evidence from nuclear ITS2 and plastid sequences

Background and Aims

The taxonomic complexity of Crataegus (hawthorn; Rosaceae, Maleae), especially in North America, has been attributed by some to hybridization in combination with gametophytic apomixis and polyploidization, whereas others have considered the roles of hybridization and apomixis to be minimal. Study of the chemical composition and therapeutic value of hawthorn extracts requires reproducible differentiation of entities that may be difficult to distinguish by morphology alone. This study sought to address this by using the nuclear ribosomal spacer region ITS2 as a supplementary DNA barcode; however, a lack of success prompted an investigation to discover why this locus gave unsatisfactory results.

Methods

ITS2 was extensively cloned so as to document inter- and intraindividual variation in this locus, using hawthorns of western North America where the genus Crataegus is represented by only two widely divergent groups, the red-fruited section Coccineae and the black-fruited section Douglasia. Additional sequence data from selected loci on the plastid genome were obtained to enhance further the interpretation of the ITS2 results.

Key Results

In the ITS2 gene tree, ribotypes from western North American hawthorns are found in two clades. Ribotypes from diploid members of section Douglasia occur in one clade (with representatives of the east-Asian section Sanguineae). The other clade comprises those from diploid and polyploid members of section Coccineae. Both clades contribute ribotypes to polyploid Douglasia. Data from four plastid-derived intergenic spacers demonstrate the maternal parentage of these allopolyploids.

Conclusions

Repeated hybridization between species of section Douglasia and western North American members of section Coccineae involving the fertilization of unreduced female gametes explains the observed distribution of ribotypes and accounts for the phenetic intermediacy of many members of section Douglasia.     

A specimen of Eocuculus Chandler, 1999 (Aves, ? Cuculidae) from the early Oligocene of France

A postcranial skeleton of a small bird from the early Oligocene locality Pichovet in Southern France is described and identified as Eocuculus cf. cherpinae Chandler, 1999. It is the second fossil record of Eocuculus which was hitherto known from a postcranial skeleton from the late Eocene of North America only. Although Eocuculus shares some derived similarities with Cuculidae (cuckoos), it distinctly differs in a number of osteological features from crown group members of this taxon. If future, more complete skeletons prove its cuculiform affinities, Eocuculus is a stem lineage representative of this taxon and not within the crown group. Recognition of Eocuculus in the early Oligocene of France provides evidence for the presence of an extinct late Eocene/early Oligocene avian taxon with an intercontinental Northern Hemisphere distribution.     

Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest

Background and Aims Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade.Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas.Key Results Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot.Conclusions This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside refugia and that range expansion from unstable areas contributes to the highest levels of plant diversity in the Bahian refugium.     

Winged Fruits of Deviacer in the Oligocene from the Ningming Basin in Guangxi,South China

Deviacer guangxiensis Chen & Manchester sp. nov. is described based on asymmetric samaras from the Oligocene Ningming Formation in Guangxi, South China, representing the first documentation of Deviacer fossils in Asia. The Oligocene species, with relatively large fruits, represents the youngest record of the genus so far known; all other records are from the Paleocene and Eocene, or late Eocene—early Oligocene in western North America and Europe. It indicates that the extinct genus, Deviacer, was widely distributed in the northern hemisphere during the Paleogene.     

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species.     

Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates

Tarsiers are small nocturnal primates with a long history of fuelling debate on the origin and evolution of anthropoid primates. Recently, the discovery of M and L opsin genes in two sister species, Tarsius bancanus (Bornean tarsier) and Tarsius syrichta (Philippine tarsier), respectively, was interpreted as evidence of an ancestral long-to-middle (L/M) opsin polymorphism, which, in turn, suggested a diurnal or cathemeral (arrhythmic) activity pattern. This view is compatible with the hypothesis that stem tarsiers were diurnal; however, a reversion to nocturnality during the Middle Eocene, as evidenced by hyper-enlarged orbits, predates the divergence of T. bancanus and T. syrichta in the Late Miocene. Taken together, these findings suggest that some nocturnal tarsiers possessed high-acuity trichromatic vision, a concept that challenges prevailing views on the adaptive origins of the anthropoid visual system. It is, therefore, important to explore the plausibility and antiquity of trichromatic vision in the genus Tarsius. Here, we show that Sulawesi tarsiers (Tarsius tarsier), a phylogenetic out-group of Philippine and Bornean tarsiers, have an L opsin gene that is more similar to the L opsin gene of T. syrichta than to the M opsin gene of T. bancanus in non-synonymous nucleotide sequence. This result suggests that an L/M opsin polymorphism is the ancestral character state of crown tarsiers and raises the possibility that many hallmarks of the anthropoid visual system evolved under dim (mesopic) light conditions. This interpretation challenges the persistent nocturnal–diurnal dichotomy that has long informed debate on the origin of anthropoid primates.     

Addicted? Reduced host resistance in populations with defensive symbionts

Heritable symbionts that protect their hosts from pathogens have been described in a wide range of insect species. By reducing the incidence or severity of infection, these symbionts have the potential to reduce the strength of selection on genes in the insect genome that increase resistance. Therefore, the presence of such symbionts may slow down the evolution of resistance. Here we investigated this idea by exposing Drosophila melanogaster populations to infection with the pathogenic Drosophila C virus (DCV) in the presence or absence of Wolbachia, a heritable symbiont of arthropods that confers protection against viruses. After nine generations of selection, we found that resistance to DCV had increased in all populations. However, in the presence of Wolbachia the resistant allele of pastrel—a gene that has a major effect on resistance to DCV—was at a lower frequency than in the symbiont-free populations. This finding suggests that defensive symbionts have the potential to hamper the evolution of insect resistance genes, potentially leading to a state of evolutionary addiction where the genetically susceptible insect host mostly relies on its symbiont to fight pathogens.     

Molecular phylogenetic evidence supports a new family of octocorals and a new genus of Alcyoniidae (Octocorallia,Alcyonacea)

Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n., and family, Parasphaerascleridae fam. n., of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites in the polyps, and have radiates or spheroidal sclerites in the colony surface and interior. Parasphaerascleridae fam. n. constitutes a well-supported clade that is phylogenetically distinct from all other octocoral taxa. We also describe a new genus of Alcyoniidae, Sphaerasclera gen. n., for a species of Eleutherobia with a unique capitate growth form. Sphaerasclera gen. n. is a member of the Anthomastus–Corallium clade of octocorals, but is morphologically and genetically distinct from Anthomastus Verrill, 1878 and Paraminabea Williams & Alderslade, 1999, two similar but dimorphic genera of Alcyoniidae that are its sister taxa. In addition, we have re-assigned two species of Eleutherobia that have clavate to capitate growth forms, polyp sclerites arranged to form a collaret and points, and spindles in the colony interior to Alcyonium, a move that is supported by both morphological and molecular phylogenetic evidence.     

Enamel thickness in the Middle Miocene great apes Anoiapithecus,Pierolapithecus and Dryopithecus

On the basis of industrial computed tomography, relative enamel thickness (RET) is computed in three Middle Miocene (ca 11.9–11.8 Ma) hominoids from Abocador de Can Mata (Vallès-Penedès Basin, Catalonia, Spain): Pierolapithecus catalaunicus from BCV1 and Anoiapithecus brevirostris from C3-Aj, interpreted as stem hominids; and Dryopithecus fontani from C3-Ae of uncertain phylogenetic affinities. Pierolapithecus displays an average RET value of 19.5, Anoiapithecus of 18.6 and Dryopithecus of 10.6. The thick-enamelled condition of Pierolapithecus and Anoiapithecus is also characteristic of afropithecids, including the more derived kenyapithecins from the early Middle Miocene of Eurasia (Griphopithecus and Kenyapithecus). Given the presence of other dentognathic and craniofacial similarities, thick enamel may be interpreted as a symplesiomorphy of the Hominidae (the great ape and human clade), which would have been later independently modified along several lineages. Given the correlation between thick enamel and hard-object feeding, our results suggest that thick enamel might have been the fundamental adaptation that enabled the out-of-Africa dispersal of great-ape ancestors and their subsequent initial radiation throughout Eurasia. The much thinner enamel of Dryopithecus is difficult to interpret given phylogenetic uncertainties, being either a hominine synapomorphy or a convergently developed feature.     

Pleiotropic regulatory genes bldA,adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin

Unlike the majority of actinomycete secondary metabolic pathways, the biosynthesis of peptidoglycan glycosyltransferase inhibitor moenomycin in Streptomyces ghanaensis does not involve any cluster-situated regulators (CSRs). This raises questions about the regulatory signals that initiate and sustain moenomycin production. We now show that three pleiotropic regulatory genes for Streptomyces morphogenesis and antibiotic production—bldA, adpA and absB—exert multi-layered control over moenomycin biosynthesis in native and heterologous producers. The bldA gene for tRNA^Leu_UAA is required for the translation of rare UUA codons within two key moenomycin biosynthetic genes (moe), moeO5 and moeE5. It also indirectly influences moenomycin production by controlling the translation of the UUA-containing adpA and, probably, other as-yet-unknown repressor gene(s). AdpA binds key moe promoters and activates them. Furthermore, AdpA interacts with the bldA promoter, thus impacting translation of bldA-dependent mRNAs—that of adpA and several moe genes. Both adpA expression and moenomycin production are increased in an absB-deficient background, most probably because AbsB normally limits adpA mRNA abundance through ribonucleolytic cleavage. Our work highlights an underappreciated strategy for secondary metabolism regulation, in which the interaction between structural genes and pleiotropic regulators is not mediated by CSRs. This strategy might be relevant for a growing number of CSR-free gene clusters unearthed during actinomycete genome mining.