13C NMR and IR analyses of structure,aging and botanical origin of Dominican and Mexican ambers

¹³C NMR analysis of Oligocene amber from the Dominican Republic, Oligo-Miocene amber from Mexico and trunk resins from certain extant species of Hymenaea, suggests a polylabdane structure for all and gives insights into structural changes during aging. Additionally, IR spectra, some aspects of the ¹³C NMR spectra and paleobotanical data suggest a close relationship between Dominican amber and H. verrucosa. By contrast, spectral evidence shows that Mexican amber differs, not only from the former polymers, but from the H. courbaril polymer.     

New Fossil Scorpion from the Chiapas Amber Lagerst?tte

A new species of scorpion is described based on a rare entire adult male preserved in a cloudy amber from Miocene rocks in the Chiapas Highlands, south of Mexico. The amber-bearing beds in Chiapas constitute a Conservation Lagerstätte with outstanding organic preservation inside plant resin. The new species is diagnosed as having putative characters that largely correspond with the genus Tityus Koch, 1836 (Scorpiones, Buthidae). Accordingly, it is now referred to as Tityus apozonalli sp. nov. Its previously unclear phylogenetic relationship among fossil taxa of the family Buthidae from both Dominican and Mexican amber is also examined herein. Preliminarily results indicate a basal condition of T. apozonalli regarding to Tityus geratus Santiago-Blay and Poinar, 1988, Tityus (Brazilotityus) hartkorni Lourenço, 2009, and Tityus azari Lourenço, 2013 from Dominican amber, as was Tityus (Brazilotityus) knodeli Lourenço, 2014 from Mexican amber. Its close relationships with extant Neotropic Tityus-like subclades such as ‘Tityus clathratus’ and the subgenus Tityus (Archaeotityus) are also discussed. This new taxon adds to the knowledge of New World scorpions from the Miocene that are rarely found trapped in amber.     

The never‐ending story of geologically ancient DNA: was the model plant Arabidopsis the source of Miocene Dominican amber?

Studies characterizing geologically ancient DNA in plants are rare, and all have reportedly obtained plastid DNA sequences from Miocene fossils in a remarkable state of preservation. Recently, a group made the extraordinary claim of having amplified a geologically ancient Miocene plastid DNA fragment (the rbcL gene) from Dominican amber nuggets, and the organismal source of this DNA was identified as Hymenaea protera (Fabaceae), the plant that produced the fossilized Dominican amber. Assuming that the Miocene sequence is error‐free, reanalysis of the sequence indicates it is probably a technical artifact or an rbcL pseudogene. Furthermore, BLAST similarity searches and phylogenetic analyses strongly suggest that the putative Miocene sequence retrieved from fossilized amber is in fact a modern contaminant from one of the most widely used model plants, Arabidopsis thaliana. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 234–240.     

Ancient butterfly-ant symbiosis: direct evidence from Dominican amber

Although symbiotic association with ants is pervasive in the butterfly families Lycaenidae and Riodinidae the age of these symbioses has never been estimated explicitly. Here we report the first known fossil riodinid caterpillar. This fossil can be dated minimally between 15 and 20 Ma old, and confidently placed in the extant genus Theope. Differing little from modern day Theope, this fossil from Dominican amber provides direct evidence that secretory and acoustical organs used by modern caterpillars to mediate symbioses with ants have been highly developed at least since the Miocene. This fossil therefore becomes the point of reference for future studies using molecular clock methods for dating these symbioses within the riodinid butterflies. Modern evidence, and the abundance of dolichoderine ants in Dominican amber (now extinct in the West Indies) imply that specialized symbiotic relationships between Theope caterpillars and these ants were likely in existence at least 15 Ma ago. The current distribution of neotropical riodinid butterfly and ant faunas indicates the extinction in the West Indies of at least two unrelated taxa that formed a tightly linked symbiotic association, which persisted to the present elsewhere. <br>     

First fossil horsefly (Diptera: Tabanidae) in Miocene Mexican amber

The fossil record of the Tabanidae is sparse when compared with other families of Diptera. Even in amber they are rare, probably because of their size and specific flight behavior. Horseflies from amber are only known from Cretaceous age New Jersey amber as well as from the Tertiary age Baltic and Dominican amber, but are herein described for the first time, with Stenotabanus oleariorum sp. n., from Mexican amber. The new species is compared to the fossil horseflies of the same genus S. brodzinskyi Lane, Poinar and Fairchild 1988 and S. woodruffi Lane and Fairchild 1989 from Dominican amber.     

Evaluating the Accuracy of Molecular Diagnostic Testing for Canine Visceral Leishmaniasis Using Latent Class Analysis

Host tissues affected by Leishmania infantum have differing degrees of parasitism. Previously, the use of different biological tissues to detect L. infantum DNA in dogs has provided variable results. The present study was conducted to evaluate the accuracy of molecular diagnostic testing (qPCR) in dogs from an endemic area for canine visceral leishmaniasis (CVL) by determining which tissue type provided the highest rate of parasite DNA detection. Fifty-one symptomatic dogs were tested for CVL using serological, parasitological and molecular methods. Latent class analysis (LCA) was performed for accuracy evaluation of these methods. qPCR detected parasite DNA in 100% of these animals from at least one of the following tissues: splenic and bone marrow aspirates, lymph node and skin fragments, blood and conjunctival swabs. Using latent variable as gold standard, the qPCR achieved a sensitivity of 95.8% (CI 90.4–100) in splenic aspirate; 79.2% (CI 68–90.3) in lymph nodes; 77.3% (CI 64.5–90.1) in skin; 75% (CI 63.1–86.9) in blood; 50% (CI 30–70) in bone marrow; 37.5% (CI 24.2–50.8) in left-eye; and 29.2% (CI 16.7–41.6) in right-eye conjunctival swabs. The accuracy of qPCR using splenic aspirates was further evaluated in a random larger sample (n = 800), collected from dogs during a prevalence study. The specificity achieved by qPCR was 76.7% (CI 73.7–79.6) for splenic aspirates obtained from the greater sample. The sensitivity accomplished by this technique was 95% (CI 93.5–96.5) that was higher than those obtained for the other diagnostic tests and was similar to that observed in the smaller sampling study. This confirms that the splenic aspirate is the most effective type of tissue for detecting L. infantum infection. Additionally, we demonstrated that LCA could be used to generate a suitable gold standard for comparative CVL testing.     

Insect outbreaks produce distinctive carbon isotope signatures in defensive resins and fossiliferous ambers

Despite centuries of research addressing amber and its various inclusions, relatively little is known about the specific events having stimulated the production of geologically relevant volumes of plant resin, ultimately yielding amber deposits. Although numerous hypotheses have invoked the role of insects, to date these have proven difficult to test. Here, we use the current mountain pine beetle outbreak in western Canada as an analogy for the effects of infestation on the stable isotopic composition of carbon in resins. We show that infestation results in a rapid (approx. 1 year) (13)C enrichment of fresh lodgepole pine resins, in a pattern directly comparable with that observed in resins collected from uninfested trees subjected to water stress. Furthermore, resin isotopic values are shown to track both the progression of infestation and instances of recovery. These findings can be extended to fossil resins, including Miocene amber from the Dominican Republic and Late Cretaceous New Jersey amber, revealing similar carbon-isotopic patterns between visually clean ambers and those associated with the attack of wood-boring insects. Plant exudate δ(13)C values constitute a sensitive monitor of ecological stress in both modern and ancient forest ecosystems, and provide considerable insight concerning the genesis of amber in the geological record.     

Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740_bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population.     

A remarkable new pygmy grasshopper (Orthoptera,Tetrigidae) in Miocene amber from the Dominican Republic

A new genus and species of pygmy grasshopper (Orthoptera: Tetrigidae) is described from Early Miocene (Burdigalian) Dominican amber. Electrotettix attenboroughi Heads & Thomas, gen. et sp. n. is assigned to the subfamily Cladonotinae based on the deeply forked frontal costa, but is remarkable for the presence of tegmina and hind wings, hitherto unknown in this subfamily.     

Pristine Early Eocene Wood Buried Deeply in Kimberlite from Northern Canada

We report exceptional preservation of fossil wood buried deeply in a kimberlite pipe that intruded northwestern Canada’s Slave Province 53.3±0.6 million years ago (Ma), revealed during excavation of diamond source rock. The wood originated from forest surrounding the eruption zone and collapsed into the diatreme before resettling in volcaniclastic kimberlite to depths >300 m, where it was mummified in a sterile environment. Anatomy of the unpermineralized wood permits conclusive identification to the genus Metasequoia (Cupressaceae). The wood yields genuine cellulose and occluded amber, both of which have been characterized spectroscopically and isotopically. From cellulose δ¹⁸O and δ²H measurements, we infer that Early Eocene paleoclimates in the western Canadian subarctic were 12–17°C warmer and four times wetter than present. Canadian kimberlites offer Lagerstätte-quality preservation of wood from a region with limited alternate sources of paleobotanical information.     

A new fossil cricket of the genus Proanaxipha in Miocene amber from the Dominican Republic (Orthoptera,Gryllidae, Pentacentrinae)

A new species of the cricket genus Proanaxipha Vickery & Poinar (Orthoptera: Gryllidae: Pentacentrinae) from Early Miocene Dominican amber is described and illustrated. Proanaxipha madgesuttonae sp. n. is distinguished from congeners by: (1) head capsule bearing a distinctive posteriorly bilobed colour spot on the vertex; (2) presence of crossveins in the proximal part of the mediocubital area; (3) apical field of tegmen entirely dark; and (4) median process of epiphallus short. The poorly known Proanaxipha bicolorata Vickery & Poinar, of questionable affinity and status, is herein regarded as a nomen inquirendum.     

The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase

Human (h) DNA repair enzyme thymine DNA glycosylase (hTDG) is a key DNA glycosylase in the base excision repair (BER) pathway that repairs deaminated cytosines and 5-methyl-cytosines. The cell cycle checkpoint protein Rad9–Rad1–Hus1 (the 9-1-1 complex) is the surveillance machinery involved in the preservation of genome stability. In this study, we show that hTDG interacts with hRad9, hRad1 and hHus1 as individual proteins and as a complex. The hHus1 interacting domain is mapped to residues 67–110 of hTDG, and Val74 of hTDG plays an important role in the TDG–Hus1 interaction. In contrast to the core domain of hTDG (residues 110–308), hTDG(67–308) removes U and T from U/G and T/G mispairs, respectively, with similar rates as native hTDG. Human TDG activity is significantly stimulated by hHus1, hRad1, hRad9 separately, and by the 9-1-1 complex. Interestingly, the interaction between hRad9 and hTDG, as detected by co-immunoprecipitation (Co-IP), is enhanced following N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) treatment. A significant fraction of the hTDG nuclear foci co-localize with hRad9 foci in cells treated with methylating agents. Thus, the 9-1-1 complex at the lesion sites serves as both a damage sensor to activate checkpoint control and a component of the BER.     

DNA Methylation Combinations in Adjacent Normal Colon Tissue Predict Cancer Recurrence: Evidence from a Clinical Cohort Study

Accumulating evidence has suggested the requirement for further stratification of patients in the same tumor stage according to molecular factors. We evaluate the combination of cancer stage and DNA methylation status as an indicator of the risk of recurrence and mortality among patients with colorectal cancer (CRC). A cohort study of 215 patients with CRC (mean age 64.32 years; 50.5% of men) from Tri-Service General Hospital in Taiwan examined the association between cancer stage and risk of CRC recurrence and mortality. A Cox proportional hazard model was used to analyze patient methylation status and clinical information at study entry, and their associations with CRC recurrence and mortality during follow-up. The advanced stage patients with p16, hMLH1, and MGMT methylation were associated with higher risk of CRC recurrence compared with the local stage patients with unmethylation status in tumor tissues, with adjusted hazard ratios (HRs) (95% confidence interval [CI]) of 9.64 (2.92–31.81), 8.29 (3.40–20.22), and 11.83 (3.49–40.12), respectively. When analyzing normal tissues, we observed similar risk of CRC recurrence with adjusted HRs (95% CI) of 10.85 (4.06–28.96), 9.04 (3.79–21.54), and 12.61 (4.90–32.44), respectively. For combined analyses, the risk of recurrence in the patients in advanced stage with DNA methylation in both normal and tumor tissues, compared with local stage with unmethylation, was increased with adjusted HR (95% CI) of 9.37 (3.36–26.09). In the advanced stage patients, methylation status and tissue subtype were associated with increased risk of 5-year cumulative CRC recurrence (p < 0.001). This study demonstrates that clustering DNA methylation status according to cancer stage and tissue subtype is critical for the assessment of risk of recurrence in CRC patients and also indicated an underlying mechanism.     

Entrapment Bias of Arthropods in Miocene Amber Revealed by Trapping Experiments in a Tropical Forest in Chiapas,Mexico

All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measurements of the trapped arthropods, and guild distribution, that the amber trap is a complex entomological trap not comparable with a single artificial trap. At the order level, the most similar trap to amber is the sticky trap. However, in the case of Diptera, at the family level, the Malaise trap is also very similar to amber. Amber captured a higher diversity of arthropods than each of the artificial traps, based on our study of Mexican amber from the Middle Miocene, a time of climate optimum, where temperature and humidity were probably higher than in modern Central America. We conclude that the size bias is qualitatively independent of the kind of trap for non–extreme values. We suggest that frequent specimens in amber were not necessarily the most frequent arthropods in the former amber forest. Selected taxa with higher numbers of specimens appear in amber because of their ecology and behavior, usually closely related with a tree–inhabiting life. Finally, changes of diversity from the Middle Miocene to Recent time in Central and South America can be analyzed by comparing the rich amber faunas from Mexico and the Dominican Republic with the fauna trapped using sticky and Malaise traps in Central America.     

A new proposal concerning the botanical origin of Baltic amber

Baltic amber constitutes the largest known deposit of fossil plant resin and the richest repository of fossil insects of any age. Despite a remarkable legacy of archaeological, geochemical and palaeobiological investigation, the botanical origin of this exceptional resource remains controversial. Here, we use taxonomically explicit applications of solid-state Fourier-transform infrared (FTIR) microspectroscopy, coupled with multivariate clustering and palaeobotanical observations, to propose that conifers of the family Sciadopityaceae, closely allied to the sole extant representative, Sciadopitys verticillata, were involved in the genesis of Baltic amber. The fidelity of FTIR-based chemotaxonomic inferences is upheld by modern–fossil comparisons of resins from additional conifer families and genera (Cupressaceae: Metasequoia; Pinaceae: Pinus and Pseudolarix). Our conclusions challenge hypotheses advocating members of either of the families Araucariaceae or Pinaceae as the primary amber-producing trees and correlate favourably with the progressive demise of subtropical forest biomes from northern Europe as palaeotemperatures cooled following the Eocene climate optimum.     

Fossil palm flowers in Dominican and Baltic amber

Five palm flowers in Dominican amber and one in Baltic amber are described or characterized. Palaeoraphe dominicana gen. et sp. nov. in the subtribe Livistoninae, is described from one perfect flower in Dominican amber. Roystonea palaea sp. nov. is described from one staminate and one pistillate flower in Dominican amber. Three other palm flowers, two perfect flowers from Dominican amber and one staminate flower from Baltic amber, are briefly characterized and figured.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 361–367.     

Arthropods in contemporary and some fossil resins

More than 4800 arthropod inclusions were isolated and identified from resin of various contemporary conifer trees in various parts of northern Eurasia. Their composition is compared with that in representative collections of Baltic and Rovno ambers (Upper Eocene) and with that in Dominican amber (Lower Miocene). The original composition of inclusions of Dominican amber is reconstructed for the first time using a procedure intended to reduce the effect of human bias. Taphonomical characteristics of resins and their effects on the composition of inclusions are studied. The actuapaleontological approach reveals a trend towards a decrease in the relative abundance of arboreal springtails and nematoceran dipterans and an increase in that of the true bugs, beetles, lepidopterans, and hymenopterans (especially ants) between the Eocene and the present. Relative abundances of spiders and mites show no clear trend. The available data on other arthropods are still insufficient for elucidating evolutionary trends. Surprisingly, a small contemporary sample from Taimyr (N. Siberia) was inexplicably more similar to the Eocene amber than to other contemporary resins. No other significant differences in composition of inclusions, compared across different conifer genera or geographic areas, have been revealed. A more detailed comparison between contemporary and fossil hymenopteran and beetle inclusions reveals correlations with both age (= evolutionary change) and geography. The absolute dominance of ants, particularly Formicinae and Myrmicinae, and, among solitary hymenopterans, Ichneumonidae, Braconidae, and Pteromalidae, and a corresponding decline in the abundance of Scelionidae and Dolichoderinae in contemporary resins compared to amber reflect evolutionary changes. In contrast, the overwhelming abundance of Formicinae and consistent occurrence of sawflies in contemporary resins of northern Eurasia appear to be explained by geography. The Eocene assemblages of beetle inclusions are characterized by a wider and more variable set of dominant families, in sharp contrast to contemporary resins, which are uniformly dominated by Curculionidae, Chrysomelidae, and Staphylinidae. Additional analyses are needed to explain this difference.     

Variation in leaf resin composition between parent tree and progeny in Hymenaea: Implications for herbivory in the humid tropics

Variation in the sesquiterpene hydrocarbon leaf resins in the tropical leguminous genus Hymenaea is compared between parent tree, seedling and sapling progeny. Relatively large discrete quantitative variation in the leaf resins, known experimentally to display little phenotypic plasticity, has been classified into Compositional Types. Differences in Compositional Types in the leaves between parent tree and their seedling and sapling progeny are more pronounced in rain forest and related eocystems than in savanna and dry forests. A model is presented in which it is suggested that this variation in leaf resin may play an important role in defence against lepidopteran herbivores and thus also in seedling establishment under Hymenaea parent trees in rain forest and related ecosystems.     

On the find of adult Micromalthus (Coleoptera, Micromalthidae) in Dominican amber

An adult of Micromalthus is discovered in amber for the first time. The species, from the Miocene Dominican amber, is described as M. anansi sp. nov., and is generally similar to Recent M. debilis, but differs in the longer legs and antennae. The Miocene species appears to be less fetalized than its modern counterpart.