scholarly journals Baltic amber Staphylinini (Coleoptera: Staphylinidae: Staphylininae): a rove beetle fauna on the eve of our modern climate

2019 ◽  
Vol 187 (1) ◽  
pp. 166-197 ◽  
Author(s):  
Adam James Brunke ◽  
Dagmara Żyła ◽  
Shûhei Yamamoto ◽  
Alexey Solodovnikov
Keyword(s):  
Large Scale ◽  
Middle Eocene ◽  
Molecular Data ◽  
Total Evidence ◽  
Baltic Amber ◽  
Phylogenetic Study ◽  
Rove Beetle ◽  
Phylogenetic Framework ◽  
Freeze Tolerant ◽  
Climate Cooling

Abstract Cenozoic climate cooling, particularly during the Eocene, has drastically shaped modern biological assemblages through a shift from an equable greenhouse to a polarized icehouse. Present-day Europe lies in a highly seasonal and temperate area that strongly embodies this modern icehouse climate. Baltic amber provides a Middle Eocene snapshot of the European fauna before this large-scale change. Here, we focused on the rove beetle tribe Staphylinini and conducted a comprehensive phylogenetic study of all known Baltic amber fossils in a total-evidence phylogenetic framework that integrates morphology with molecular data from six gene fragments. Based on our well-resolved topology, we propose the following: †Baltognathina subtrib. nov., Afroquediina subtrib. nov., Antimerina subtrib. nov., †Baltognathus aenigmaticus gen. et sp. nov., †Eolophorus gen. nov., †Laevisaurus robustus and †Laevisaurus gracilis gen. et spp. nov., †Hemiquedius europaeus sp. nov. and †Bolitogyrus fragmentus sp. nov. †Quedius cretaceus is placed as junior synonym of †Cretoquedius infractus. The earliest definitive fossils of Quediina are reported herein from the Eocene. The Staphylinini fauna of Middle Eocene Europe combined thermophilic, freeze-intolerant lineages with freeze-tolerant, temperate lineages and, unlike most other staphylinid or beetle lineages, all have since become extinct in the Palaearctic region.

scholarly journals A total-evidence approach resolves phylogenetic placement of ‘Cafius’ gigas, a unique recently extinct rove beetle from Lord Howe Island

2020 ◽  
Author(s):  
Arn Rytter Jensen ◽  
Josh Jenkins Shaw ◽  
Dagmara Żyła ◽  
Alexey Solodovnikov
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
New Combination ◽  
Phylogenetic Placement ◽  
Lord Howe Island ◽  
Rove Beetle ◽  
Morphological And Molecular Data

Abstract Cafius gigas Lea, 1929 (Coleoptera: Staphylinidae) was a large rove beetle endemic to Lord Howe Island (LHI) resembling Cafius and the LHI flightless endemic Hesperus dolichoderes (Lea, 1925). Like several other LHI endemics, C. gigas became extinct due to human-introduced rats. It is a legacy species valuable for understanding the LHI biota in terms of evolutionary biology and historical biogeography. Whether C. gigas was a member of Cafius Curtis, 1829, restricted to oceanic shores and prone to trans-oceanic dispersal, or related to H. dolichoderes, would have different implications. We subjected C. gigas to a total-evidence phylogenetic analyses of morphological and molecular data using model-based and parsimony methods. As a result, it is transferred to Hesperus Fauvel, 1874 with the new combination Hesperus gigas (Lea, 1929) comb. nov. Our analysis indicates that the montane leaf litter inhabitant H. gigas evolved neither in situ nor from a seashore Cafius-ancestor, or from an ancestor shared by two other LHI endemic congeners, Hesperus pacificus Olliff, 1887 and H. dolichoderes. It also suggests that all three Hesperus species that currently occur on LHI could have evolved on various seamounts at various times before reaching LHI.

scholarly journals Dipole patterns in tropical precipitation were pervasive across landmasses throughout Marine Isotope Stage 5

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Katrina Nilsson-Kerr ◽  
Pallavi Anand ◽  
Philip B. Holden ◽  
Steven C. Clemens ◽  
Melanie J. Leng
Keyword(s):  
Large Scale ◽  
Marine Isotope Stage ◽  
Convergence Zone ◽  
Inter Tropical Convergence Zone ◽  
Tropical Regions ◽  
Tropical Precipitation ◽  
Rainfall Patterns ◽  
Marine Isotope Stage 5 ◽  
Climate Cooling ◽  
The Tropics

AbstractMost of Earth’s rain falls in the tropics, often in highly seasonal monsoon rains, which are thought to be coupled to the inter-hemispheric migrations of the Inter-Tropical Convergence Zone in response to the seasonal cycle of insolation. Yet characterization of tropical rainfall behaviour in the geologic past is poor. Here we combine new and existing hydroclimate records from six large-scale tropical regions with fully independent model-based rainfall reconstructions across the last interval of sustained warmth and ensuing climate cooling between 130 to 70 thousand years ago (Marine Isotope Stage 5). Our data-model approach reveals large-scale heterogeneous rainfall patterns in response to changes in climate. We note pervasive dipole-like tropical precipitation patterns, as well as different loci of precipitation throughout Marine Isotope Stage 5 than recorded in the Holocene. These rainfall patterns cannot be solely attributed to meridional shifts in the Inter-Tropical Convergence Zone.

scholarly journals Late oligocene–early miocene shortening in the Thrace Basin, northern Aegean

2021 ◽  
Author(s):  
Ümitcan Erbil ◽  
Aral I. Okay ◽  
Aynur Hakyemez
Keyword(s):  
Large Scale ◽  
Middle Eocene ◽  
Early Miocene ◽  
Fold Axis ◽  
Late Oligocene ◽  
The Balkans ◽  
Sedimentary Sequences ◽  
The North ◽  
Early Oligocene ◽  
Thrace Basin

AbstractLate Cenozoic was a period of large-scale extension in the Aegean. The extension is mainly recorded in the metamorphic core complexes with little data from the sedimentary sequences. The exception is the Thrace Basin in the northern Aegean, which has a continuous record of Middle Eocene to Oligocene marine sedimentation. In the Thrace Basin, the Late Oligocene–Early Miocene was characterized by north-northwest (N25°W) shortening leading to the termination of sedimentation and formation of large-scale folds. We studied the stratigraphy and structure of one of these folds, the Korudağ anticline. The Korudağ anticline has formed in the uppermost Eocene–Lower Oligocene siliciclastic turbidites with Early Oligocene (31.6 Ma zircon U–Pb age) acidic tuff beds. The turbidites are underlain by a thin sequence of Upper Eocene pelagic limestone. The Korudağ anticline is an east-northeast (N65°E) trending fault-propagation fold, 9 km wide and 22 km long and with a subhorizontal fold axis. It is asymmetric with shallowly-dipping northern and steeply-dipping southern limbs. Its geometry indicates about 1 km of shortening in a N25°W direction. The folded strata are unconformably overlain by Middle Miocene continental sandstones, which constrain the age of folding. The Korudağ anticline and other large folds in the Thrace Basin predate the inception of the North Anatolian Fault (NAF) by at least 12 myr. The Late Oligocene–Early Miocene (28–17 Ma) shortening in the Thrace Basin and elsewhere in the Balkans forms an interlude between two extensional periods, and is probably linked to changes in the subduction dynamics along the Hellenic trench.

scholarly journals Charcoal in soils of the Allerød-Younger Dryas transition were the result of natural fires and not necessarily the effect of an extra-terrestrial impact

2008 ◽  
Vol 87 (4) ◽  
pp. 359-361 ◽  
Author(s):  
T. van der Hammen ◽  
B. van Geel
Keyword(s):  
North America ◽  
Large Scale ◽  
Sand Dunes ◽  
Younger Dryas ◽  
Natural Fires ◽  
Water Tables ◽  
Pine Trees ◽  
Climate Cooling ◽  
Fossil Records ◽  
Terrestrial Material

AbstractDuring the warm Bølling-Allerød interstadial, tree species migrated from their refugia in southern Europe northwards into the area within the present temperate climatic zone. It is evident from high levels of charcoal in fossil records in this region that, especially during the later part of the Bølling-Allerød interstadial, many fires occurred. The start of the Younger Dryas was characterised by rapid and intense cooling and rising water tables, with catastrophic effects on the vegetation. Thermophilous pine trees could not survive the cold Younger Dryas climate. Dead wood provided an abundant source of fuel for intense, large-scale fires seen in many records as a concentration of charcoal particles in so-called ’Usselo-soils’ dated to ca 10,95014C BP. A similar trend in increased charcoal indicating increased burning is seen at many sites across North America at this time and it has been suggested by Firestone et al. (2007) that this was caused by an explosion of extra-terrestrial material over northern North America, causing the Younger Dryas climate cooling and Megafaunal extinction. We argue that there is no need to invoke an extraterrestrial cause to explain the charcoal in the fossilized soils. The volume of forest trees that died as a result of the cold Younger Dryas climate would easily have supplied sufficient fuel for intense, large-scale fires and can be used to account for the concentration of charcoal particles. As soils were no longer covered by dense vegetation, much erosion occurred during the Younger Dryas and therefore, at many places, Usselo soils, rich in charcoal, were preserved under aeolian sand dunes.

Late Paleogene paleotopographic evolution of the northern Cordilleran orogenic front: Implications for demise of the orogen

2021 ◽  
Author(s):  
Majie Fan ◽  
Kurt N. Constenius ◽  
Rachel F. Phillips ◽  
David L. Dettman
Keyword(s):  
Initial Phase ◽  
Middle Eocene ◽  
High Elevation ◽  
Late Eocene ◽  
Crustal Extension ◽  
Late Oligocene ◽  
Slab Rollback ◽  
Basin Floor ◽  
Climate Cooling ◽  
High Range

The paleotopographic history of the North American Cordilleran orogen holds the key to understanding mechanisms of orogenesis and subsequent orogenic collapse. It has been suggested that the orogenic front in western Montana (USA) and Alberta (Canada) was more than 4 km high during Late Cretaceous−early Eocene contractional deformation and during the initial phase of extension in the middle Eocene; however, the late Eocene−Oligocene topographic evolution during continued extensional collapse remains poorly constrained. Here we extend the paleotopographic record in the Kishenehn Basin in northwestern Montana and southeastern British Columbia (Canada) to the late Oligocene by studying δ18O values of fossil mollusks and cement and paleosol carbonates. The molluscan taxa changed from three sympatric groups with preferred habitats ranging from tropical wet, semi-arid subtropical, and temperate during the middle and late Eocene, to mainly a single group associated with temperate environment during the Oligocene, reflecting a decline in molluscan biodiversity induced by climate cooling across the Eocene−Oligocene transition. Reconstructed δ18O values of alpine snowmelt and basinal precipitation decreased by 1.4‰ and 3.8‰, respectively, from the middle to late Eocene, reflecting climate cooling and ∼1 km surface uplift of the basin floor. The reconstructed alpine snowmelt δ18O values then increased by 2.9‰ in the Oligocene suggesting a ∼0.5 km drop in elevation of the orogenic front. Collectively, the results of our new and previously published δ18O data chronicle the paleotopographic response to the change from flat-slab subduction to slab rollback over a 45 m.y. period. These data suggest that the orogenic front was characterized by high elevation (>4 km) in the ancestral Lewis-Clark-Livingston ranges during latest Cretaceous−early Eocene (ca. 75−52 Ma) contraction. The initial phase of extension related to the Kishenehn Basin created a lowland basin with a surface elevation of only ∼1.5 km during the early middle Eocene (ca. 46−44 Ma) whereas the ranges remained >4 km high. The high range elevations were sustained for at least 12 m.y. in the middle to late Eocene concurrent with extension, while the basin floor elevation was uplifted to ∼2.5 km by the latest Eocene (ca. 36−34 Ma). Basin aggradation can explain at most half of the 1 km basin floor uplift. The remaining amount (at least 0.5 km) and sustained high range elevation suggest that range denudation and crustal extension was compensated by the isostatic and thermal effects of slab rollback and/or passage of a slab window and infusion of hot asthenosphere beneath the continent. The range elevation in the orogenic front decreased ∼0.5 km by the late Oligocene (ca. 28 Ma), associated with a decrease in rock uplift rate associated with extension. A post-Oligocene elevation drop of ∼1 km resulted in both the ranges and basin floor reaching modern topography in the Kishenehn Basin drainage, likely due to the regional effect of Neogene Basin and Range extension. This study, along with the previous investigation of the Kishenehn Basin by Fan et al. (2017), are the first studies that systematically investigate paleorelief of the orogenic belt by reconstructing paleoelevations of the mountains and the basin at the same time. The results highlight that the Cordilleran orogenic front of northern Montana and southern British Columbia sustained its high elevation edifice for at least 12 m.y. after the start of extension. We suggest that initial crustal extension did not result in orogenic demise because of concurrent thermal and isostatic uplift.

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

2008 ◽  
Vol 98 (5) ◽  
pp. 499-507 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Host Specificity ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Primary Host ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

scholarly journals Mol-BERT: An Effective Molecular Representation with BERT for Molecular Property Prediction

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Juncai Li ◽  
Xiaofei Jiang
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Large Scale ◽  
Molecular Data ◽  
Molecular Property ◽  
Property Prediction ◽  
Learning Framework ◽  
Learning Techniques ◽  
Potential Benefits ◽  
Current Sequence

Molecular property prediction is an essential task in drug discovery. Most computational approaches with deep learning techniques either focus on designing novel molecular representation or combining with some advanced models together. However, researchers pay fewer attention to the potential benefits in massive unlabeled molecular data (e.g., ZINC). This task becomes increasingly challenging owing to the limitation of the scale of labeled data. Motivated by the recent advancements of pretrained models in natural language processing, the drug molecule can be naturally viewed as language to some extent. In this paper, we investigate how to develop the pretrained model BERT to extract useful molecular substructure information for molecular property prediction. We present a novel end-to-end deep learning framework, named Mol-BERT, that combines an effective molecular representation with pretrained BERT model tailored for molecular property prediction. Specifically, a large-scale prediction BERT model is pretrained to generate the embedding of molecular substructures, by using four million unlabeled drug SMILES (i.e., ZINC 15 and ChEMBL 27). Then, the pretrained BERT model can be fine-tuned on various molecular property prediction tasks. To examine the performance of our proposed Mol-BERT, we conduct several experiments on 4 widely used molecular datasets. In comparison to the traditional and state-of-the-art baselines, the results illustrate that our proposed Mol-BERT can outperform the current sequence-based methods and achieve at least 2% improvement on ROC-AUC score on Tox21, SIDER, and ClinTox dataset.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Expansion and diversification of high-latitude radiolarian assemblages in the late Eocene linked to a cooling event in the Southwest Pacific

2015 ◽  
Vol 11 (4) ◽  
pp. 2977-3018 ◽  
Author(s):  
K. M. Pascher ◽  
C. J. Hollis ◽  
S. M. Bohaty ◽  
G. Cortese ◽  
R. M. McKay
Keyword(s):  
Oxygen Isotope ◽  
High Latitude ◽  
Large Scale ◽  
Middle Eocene ◽  
Late Eocene ◽  
Climate History ◽  
Southwest Pacific ◽  
Early Oligocene ◽  
Radiolarian Assemblages

Abstract. The Eocene was characterised by "greenhouse" climate conditions that were gradually terminated by a long-term cooling trend through the middle and late Eocene. This long-term trend was determined by several large-scale climate perturbations that culminated in a shift to "ice-house" climates at the Eocene–Oligocene Transition. Geochemical and micropaleontological proxies suggest that tropical-to-subtropical sea-surface temperatures persisted into the late Eocene in the high-latitude Southwest Pacific Ocean. Here, we present radiolarian microfossil assemblage and foraminiferal oxygen and carbon stable isotope data from Deep Sea Drilling Project (DSDP) Sites 277, 280, 281 and 283 from the middle Eocene to early Oligocene (~ 40–33 Ma) to identify oceanographic changes in the Southwest Pacific across this major transition in Earth's climate history. The Middle Eocene Climatic Optimum at ~ 40 Ma is characterised by a negative shift in foraminiferal oxygen isotope values and a radiolarian assemblage consisting of about 5 % of low latitude taxa Amphicraspedum prolixum group and Amphymenium murrayanum. In the early late Eocene at ~ 37 Ma, a positive oxygen isotope shift can be correlated to the Priabonian Oxygen Isotope Maximum (PrOM) event – a short-lived cooling event recognized throughout the Southern Ocean. Radiolarian abundance, diversity, and preservation increase during the middle of this event at Site 277 at the same time as diatoms. The PrOM and latest Eocene radiolarian assemblages are characterised by abundant high-latitude taxa. These high-latitude taxa also increase in abundance during the late Eocene and early Oligocene at DSDP Sites 280, 281 and 283 and are associated with very high diatom abundance. We therefore infer a~northward expansion of high-latitude radiolarian taxa onto the Campbell Plateau towards the end of the late Eocene. In the early Oligocene (~ 33 Ma) there is an overall decrease in radiolarian abundance and diversity at Site 277, and diatoms are absent. These data indicate that, once the Tasman Gateway was fully open in the early Oligocene, a frontal system similar to the present day was established, with nutrient-depleted subantarctic waters bathing the area around DSDP Site 277, resulting in a more oligotrophic siliceous plankton assemblage.

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