Post-Eocene coupled oroclines in the Talesh (NW Iran): paleomagnetic constraints

The Talesh Mountains (NW Iran) witnessed a long deformation history from the Triassic Cimmerian orogeny to the ongoing Arabia-Eurasia collision. This protracted multi-stage deformation has generated a remarkably curved orogen with a puzzling kinematic and deformational history. In this study, we investigate the origin of the Talesh curvature through paleomagnetic analyses on rocks of Paleozoic, Mesozoic and Cenozoic age. Our results indicate that at least two major, large-scale, vertical-axis-rotations took place since the Late Cretaceous: 1) a pre-Eocene 73° ± 17° clockwise rotation and 2) post-Eocene differential rotations that formed the Z-shaped mountain belt within a crustal-scale shear zone. The latter involved an increasing amount of clockwise (CW) rotation from south (16°) to north (48°). The orocline formation likely started during the Oligocene where an approximately east-west oriented mountain belt was buckled by the Arabia-Eurasia collision, with Arabia acting as a rigid indenter and the South Caspian basin as a rigid backstop. We hypothesise that the NE-SW oriented Aras and Lahijan fault zones, inherited from transform faults related to the Mesozoic opening of the Caspian-Black Sea back-arc, accommodated the coupled orocline formation

Neoadjuvant nivolumab and nivolumab plus ipilimumab induce (near-) complete responses in patients with head and neck squamous cell carcinoma:The IMCISION trial

BackgroundNivolumab (NIVO) alone or with ipilimumab (COMBO) immune checkpoint blockade (ICB) prior to curative surgery has shown promising results in multiple tumor types. We completed a phase Ib/II study with neoadjuvant NIVO or COMBO in resectable head and neck squamous cell carcinoma (HNSCC) and show safety, efficacy and correlative biomarker results.Methods32 stage II-IVB HNSCC patients indicated for curative (salvage) surgery were treated with NIVO (240mg, weeks 1&3, N=6) or NIVO (240mg, weeks 1&3) + IPI (1mg/kg, week 1, N=26) prior to surgery in week 5. Imaging was performed at baseline and week 4. AEs were reported in terms of CTCAE. Pathological response (pR) was defined as % change in viable tumor cells from baseline to on-treatment; ≥90% pR was considered (near-) complete response (pCR). WES and RNAseq were performed on paired tumor biopsies.Results32 (31 HPV-negative) patients started treatment (stage II n=3, III n=8, IVA-B n=11, recurrent disease n=10). 6 patients included with recurrent disease had had previous (C)RT. 1 patient discontinued ICB after one course due to patient’s preference. Surgery was not postponed in any patient. 3/32 patients did not undergo surgery: 1 due to unresectable PD and 2 due to reasons unrelated to ICB or disease. Grade 3-4 irAEs in 11/32 patients were well manageable. (Near-)pCR in the primary tumor was seen in 9/29 evaluable patients (31%). Another 31% of patients had 20-89% pR. At 14 months median FU, RFS for patients with (near-)pCR was 100%, significantly better than patients with <90% pR (p=<0.05). Metabolic response assessment with FDG-PET (week 4) was able to identify (near-)pCRs. A baseline AID/APOBEC-associated tumor mutational profile was correlated with (near)pCR (p=<0.05). Finally, (near)pCR tumors were characterized by a decrease in hypoxia gene expression after ICB.ConclusionsNeoadjuvant ICB was feasible in HNSCC and induced (near)pCR in 31% of evaluable patients at time of surgery, which was accompanied by 100% RFS. Baseline AID/APOBEC-related mutations, on-treatment FDG-PET and resolution of hypoxia need future validation to discover their potential role as biomarkers for (near)pCR after ICB in HNSCC

Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes

Background: Due to their great species and ecological diversity as well as their capacity to produce hundreds of different toxins, cone snails are of interest to evolutionary biologists, pharmacologists and amateur naturalists alike. Taxonomic identification of cone snails still relies mostly on the shape, color, and banding patterns of the shell. However, these phenotypic traits are prone to homoplasy. Therefore, the consistent use of genetic data for species delimitation and phylogenetic inference in this apparently hyperdiverse group is largely wanting. Here, we reconstruct the phylogeny of the cones endemic to Cabo Verde archipelago, a well-known radiation of the group, using mitochondrial (mt) genomes. Results: The reconstructed phylogeny grouped the analyzed species into two main clades, one including Kalloconus from West Africa sister to Trovaoconus from Cabo Verde and the other with a paraphyletic Lautoconus due to the sister group relationship of Africonus from Cabo Verde and Lautoconus ventricosus from Mediterranean Sea and neighboring Atlantic Ocean to the exclusion of Lautoconus endemic to Senegal (plus Lautoconus guanche from Mauritania, Morocco, and Canary Islands). Within Trovaoconus, up to three main lineages could be distinguished. The clade of Africonus included four main lineages (named I to IV), each further subdivided into two monophyletic groups. The reconstructed phylogeny allowed inferring the evolution of the radula in the studied lineages as well as biogeographic patterns. The number of cone species endemic to Cabo Verde was revised under the light of sequence divergence data and the inferred phylogenetic relationships. Conclusions: The sequence divergence between continental members of the genus Kalloconus and island endemics ascribed to the genus Trovaoconus is low, prompting for synonymization of the latter. The genus Lautoconus is paraphyletic. Lautoconus ventricosus is the closest living sister group of genus Africonus. Diversification of Africonus was in allopatry due to the direct development nature of their larvae and mainly triggered by eustatic sea level changes during the Miocene-Pliocene. Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half.Spanish Ministry of Science and Innovation [CGL2013-45211-C2-2-P, CGL2016-75255-C2-1-P, BES-2011-051469, BES-2014-069575, Doctorado Nacional-567]info:eu-repo/semantics/publishedVersio

High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using affymetrix cytoscan HD chip

Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples. © 2014 Yu et al

Quaternary time scales for the Pontocaspian domain: interbasinal connectivity and faunal evolution

The Pontocaspian (Black Sea - Caspian Sea) region has a very dynamic history of basin development and biotic evolution. The region is the remnant of a once vast Paratethys Sea. It contains some of the best Eurasian geological records of tectonic, climatic and paleoenvironmental change. The Pliocene-Quaternary co-evolution of the Black Sea-Caspian Sea is dominated by major changes in water (lake and sea) levels resulting in a pulsating system of connected and isolated basins. Understanding the history of the region, including the drivers of lake level and faunal evolution, is hampered by indistinct stratigraphic nomenclature and contradicting time constraints for regional sedimentary successions. In this paper we review and update the late Pliocene to Quaternary stratigraphic framework of the Pontocaspian domain, focusing on the Black Sea Basin, Caspian Basin, Marmara Sea and the terrestrial environments surrounding these large, mostly endorheic lake-sea systems

Probing Tectonic Topography in the Aftermath of Continental Convergence in Central Europe

Continental topography is at the interface of processes taking place at depth in the Earth,at its surface,and above it.Topography influences society, not only in terms of slow processes of landscape change and earthquakes,but also in terms of how it affects climate.The Pannonian Basin–Carpathian Orogen System in Central and Eastern Europe represents a key natural laboratory for the development of a new generation of models for ongoing orogeny and its effect on continental topography development (Figure 1).This system comprises some of the best documented sedimentary basins in the world,located within the Alpine orogenic belt, at the transition between the western European lithosphere and the East European Craton. It includes one of the most active seismic zones in Europe,with intermediate depth (50–220 km) mantle earthquakes of significant magnitude occurring in a geographically restricted area in the Vrancea zone of southeastern Romania

Historical Isolation versus Recent Long-Distance Connections between Europe and Africa in Bifid Toadflaxes (Linaria sect. Versicolores)

Background: Due to its complex, dynamic and well-known paleogeography, the Mediterranean region provides an ideal framework to study the colonization history of plant lineages. The genus Linaria has its diversity centre in the Mediterranean region, both in Europe and Africa. The last land connection between both continental plates occurred during the Messinian Salinity Crisis, in the late Miocene (5.96 to 5.33 Ma). Methodology/Principal Findings: We analyzed the colonization history of Linaria sect. Versicolores (bifid toadflaxes), which includes c. 22 species distributed across the Mediterranean, including Europe and Africa. Two cpDNA regions (rpl32-trnL UAG and trnK-matK) were sequenced from 66 samples of Linaria. We conducted phylogenetic, dating, biogeographic and phylogeographic analyses to reconstruct colonization patterns in space and time. Four major clades were found: two of them exclusively contain Iberian samples, while the other two include northern African samples together with some European samples. The bifid toadflaxes have been split in African and European clades since the late Miocene, and most lineage and speciation differentiation occurred during the Pliocene and Quaternary. We have strongly inferred four events of post-Messinian colonization following long-distance dispersal from northern Africa to the Iberian Peninsula, Sicily and Greece. Conclusions/Significance: The current distribution of Linaria sect. Versicolores lineages is explained by both ancien

Palaeoclimatic events, dispersal and migratory losses along the Afro-European axis as drivers of biogeographic distribution in Sylvia warblers

<p>Abstract</p> <p>Background</p> <p>The Old World warbler genus <it>Sylvia </it>has been used extensively as a model system in a variety of ecological, genetic, and morphological studies. The genus is comprised of about 25 species, and 70% of these species have distributions at or near the Mediterranean Sea. This distribution pattern suggests a possible role for the Messinian Salinity Crisis (from 5.96-5.33 Ma) as a driving force in lineage diversification. Other species distributions suggest that Late Miocene to Pliocene Afro-tropical forest dynamics have also been important in the evolution of <it>Sylvia </it>lineages. Using a molecular phylogenetic hypothesis and other methods, we seek to develop a biogeographic hypothesis for <it>Sylvia </it>and to explicitly assess the roles of these climate-driven events.</p> <p>Results</p> <p>We present the first strongly supported molecular phylogeny for <it>Sylvia</it>. With one exception, species fall into one of three strongly supported clades: one small clade of species distributed mainly in Africa and Europe, one large clade of species distributed mainly in Africa and Asia, and another large clade with primarily a circum-Mediterranean distribution. Asia is reconstructed as the ancestral area for <it>Sylvia</it>. Long-distance migration is reconstructed as the ancestral character state for the genus, and sedentary behavior subsequently evolved seven times.</p> <p>Conclusion</p> <p>Molecular clock calibration suggests that <it>Sylvia </it>arose in the early Miocene and diverged into three main clades by 12.6 Ma. Divergence estimates indicate that the Messinian Salinity Crisis had a minor impact on <it>Sylvia</it>. Instead, over-water dispersals, repeated loss of long-distance migration, and palaeo-climatic events in Africa played primary roles in <it>Sylvia </it>divergence and distribution.</p

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora

Reconciling Deep Calibration and Demographic History: Bayesian Inference of Post Glacial Colonization Patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758)

A precise inference of past demographic histories including dating of demographic events using Bayesian methods can only be achieved with the use of appropriate molecular rates and evolutionary models. Using a set of 596 mitochondrial cytochrome c oxidase I (COI) sequences of two sister species of European green crabs of the genus Carcinus (C. maenas and C. aestuarii), our study shows how chronologies of past evolutionary events change significantly with the application of revised molecular rates that incorporate biogeographic events for calibration and appropriate demographic priors. A clear signal of demographic expansion was found for both species, dated between 10,000 and 20,000 years ago, which places the expansions events in a time frame following the Last Glacial Maximum (LGM). In the case of C. aestuarii, a population expansion was only inferred for the Adriatic-Ionian, suggestive of a colonization event following the flooding of the Adriatic Sea (18,000 years ago). For C. maenas, the demographic expansion inferred for the continental populations of West and North Europe might result from a northward recolonization from a southern refugium when the ice sheet retreated after the LGM. Collectively, our results highlight the importance of using adequate calibrations and demographic priors in order to avoid considerable overestimates of evolutionary time scales