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FIGURE 5. Main differences between genera Amiracarus Miko n in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 5. Main differences between genera Amiracarus Miko n. gen. (A–C) and Miracarus Kunst 1959 (D–F), based on the type species (Amiracarus senensis—left, Miracarus hurkai—right, reconstructed from holotype figure, see Fig. 1). Dorsal view of whole body (A and D): proportion between length of prodorsum and length of notogaster (grey arrows); proportion of width of prodorsum and width of notogaster (black arrows); position of interlamellar setae; form of pteromorphs; position of seta e2—in relation to setae in row c2–cp–e2–f2; position of the seta h3—in relation to the seta in row h –h2–h3. Lateral view of anterior part of the body (B and E): form of pteromorph; development of tutoria and tutorial cusps; size and form of pedotectum I. Development of the sensilus (C and F).

FIGURE 2 in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 2. Amiracarus senensis (Bernini 1975) n. comb. (fossil individual from sediments of cave Ponicova, Romania). A—dorsal view; B—ventral view; C—lateral view; D—detail of tutorium; E—sensilus. Legs missing, only trochanters III and IV remained preserved. Bar indicating 100 µm (A, B, C). Abbreviation: ao—anal opening, cgl— circumgastric line, cpl—circumpedal line, dis—discidium, go—genital opening, lam—lamella, mt– mentotectum, pd1— pedotectum I, pd2—pedotectum II, pt—pteromorph, R—acetabular protrusion of leg III, sl—notogastral lateromedial furrow, ss—sensillus, trIV—trochanter IV, tu—tutorium, tu1—tutorial carina 1, tu2—tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.

FIGURE 6 in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 6. Fossil material of Amiracarus pliocennatus Miko, n. gen., n. sp. Upper row—original photographs of Oana Moldovan, published here to allow matching with individuals as reported in Moldovan et al. (2011): A—holotype from Trhlovca Cave, Slovenia (reported in Moldovan et al. (2011) as Miracarus sp. on Fig. 3A, Fig. 5 and Tab 2 (both in Pliocene sections), B–C—paratypes from Račiška pečina Cave in Slovenia (individuals reported in Moldovan et al. (2011) Miracarus sp. on Fig. 5 and Tab 2 in Pleistocene sections; individual under B was later lost so the more recent photographs are not available). Bars indicating 100 µm. Middle row—Amiracarus pliocennatus Miko, n. gen., n. sp., holotype (same individual as sub A): D—dorsal view, E—ventral view, F—lateral view. Bars indicating 50 µm. Lower row—A. pliocennatus Miko, n. gen., n. sp., paratype (same individual as sub C): G—dorsal view, H—ventral view, I— lateral view. Bars indicating 50 µm.

FIGURE 4. Amiracarus pliocennatus Miko, n in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 4. Amiracarus pliocennatus Miko, n. sp. (A–B, E paratype from Račiška pečina Cave, Slovenia; F— holotype). A—prodorsum of paratype from dorsal view; B—ventral view of paratype; C—variability of sensillus in paratypes; D—variability of lamellar cuspis, holotype right; E—detail of podosoma, ventral view. Bar indicating 100 µm (A, B). Abbreviations: cpl—circumpedal line, dis—discidium, ku—carina ku on pedotectum I, pd1—pedotectum I, pd2—pedotectum II, R—acetabular protrusion of leg III, tsI—trochanteral seta I, tsII—trochanteral seta II. Rest represents names of setae or setal insertions and lyrifissures.

FIGURE 1. Miracarus hurkai Kunst, 1959 in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 1. Miracarus hurkai Kunst, 1959 (holotype). A—dorsal view (without legs); B—ventral view (legs only partly depicted); C—dorsolateral view of prodorsum (notogaster and ventral structures only partly sketched); D—detailed view of sensillus. Bar indicating 100 µm (A, B, C). Abbreviations: an—anal plate, cgl—circumgastric line, cpl—circumpedal line, dis—discidium, g—genital plate, lam—lamella, mt—mentotectum, pd1—pedotectum I, pd2—pedotectum II, pt— pteromorph, R—acetabular protrusion of leg III, ro—rostrum, sl—notogastral lateromedial furrow, ss—sensillus, TrIII— trochanter III, Tr IV—trochanter IV, tsII—trochanteral seta II, tu—tutorium, tu1—tutorial carina 1, tu2—tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.

FIGURE 3. Amiracarus pliocennatus Miko, n in Oribatid mite fossils from pre-Quaternary sediments in Slovenian caves II. Amiracarus pliocennatus n.gen., n.sp. (Microzetidae) from Pliocene, with comments on the other species of the genus

FIGURE 3. Amiracarus pliocennatus Miko, n. sp. (A–C, E holotype from Trhlovca Cave, Slovenia; D—paratype from Račiška pečina Cave, Slovenia). A—dorsal view; B—ventral view (part); C—lateral view of prodorsum and podosoma; D—ventral view of camerostome and rostrum; E—detail of rostrum, dorsolateral view. Bars indicating 50 µm (A, C), 100 µm (B) and 25 µm (D). Abbreviations: cgl—circumgastric line, cpl—circumpedal line, dis—discidium, inc—rostral incision, lam—lamella, mt—mentotectum, pd1—pedotectum I, pd2—pedotectum II, pt—pteromorph, R—acetabular protrusion of leg III, rc—rostral carina, ru—rutellum, sl—notogastral lateromedial furrow, ss—sensillus, TrIII— trochanter III, Tr IV—trochanter IV, tsI—trochanteral seta I, tsII—trochanteral seta II, tu1—tutorial carina 1, tu2— tutorial carina 2, tu3—tutorial carina 3. Rest represents names of setae or setal insertions and lyrifissures.

opencc-by-4.0Nov 2024View details →

Interpolated Quaternary and Jurassic surfaces below a 4.5 m dextral railroad offset near Summerville, SC

Oblique view of the detrended morphology of the base of the Quaternary encountered in shallow auger holes in a ±30 km region near Summerville South Carolina (Weems and Lewis, 2002, Weems et al., 2014) and smoothed morphology of the prominent Jurassic reflector from reflection profiles from Chapman and Beales (2011). The smoothed Jurassic reflector is encountered at 560-850 m depth (Vert.= Hor. Scale x50); The Quaternary horizon lies at 3-9 m depth and its vertical scale is exagerrated x 5000. The vertical Summerville/ Gants fault is depicted with two colors. A dislocation model fit to a 4.5 m, 1.5 km scale dextral offset to the railroad (black line crossing the fault) shows that it slipped below ≈450 m, and this part of the fault is shaded red.  Also shown with a broken dashed line are the eastern and southern edges of the Pneholoway Marine Terrace. The movie rotates about a point near Summerville that was raised by ≈1 m in the earthquake, and illustrates the coincidence of the upwarped base of the Quaternary and the Summerville/Gants fault,  suggesting that the eastern edge of the Penholoway Terrace has been raised a few meters by earthquakes prior to the 1886 Charleston earthquake.

opencc-by-4.0Oct 2021View details →

Fast response of Amazon rivers to Quaternary climate cycles

Data table of Amazon rivers. Data sources are described in section 2.2 of the accompanying manuscript.

opencc-by-4.0Jul 2021View details →

Automatic exhaustive calculations of large material space by Korringa-Kohn-Rostoker coherent approximation method --- Applied to equiatomic quaternary high entropy alloys

Calculated data of equiatomic quaternary solid solution phase (high-entropy alloys) on local magnetic moment, total magnetization, magnetic phase transition temperature and residual resistivity. The data was added on October 28.

dryad32/100

Data from: Reintroducing extirpated herbivores could partially reverse the late Quaternary decline of large and grazing species

Aim: Reinstating large, native herbivores is an essential component of ecological restoration efforts, as these taxa can be important drivers of ecological processes. However, many herbivore species have gone globally or regionally extinct during the last 50,000 years, leaving simplified herbivore assemblages and trophically downgraded ecosystems. Here, we discuss to what extent trophic rewilding can undo these changes by reinstating native herbivores. Location: Global Time Period: We report functional trait changes from the Late Pleistocene to the present, and estimated trait changes under future scenarios. Major Taxa Studied: Wild, large (≥10 kg), terrestrial, mammalian herbivores Methods: We use a functional trait dataset containing all late Quaternary large herbivores ≥10 kg to look at changes in the body mass and diet composition of herbivore assemblages, a proxy for species' ecological effects. First, we assess how these traits have changed from the Late Pleistocene to the present. Next, we quantify how the current body mass and diet composition would change if all extant, wild herbivores were restored to their native ranges (and if no functional replacements were used), exploring scenarios with different baselines. Results: Defaunation has primarily removed large and grazing herbivores. Reinstating extant herbivores across their native ranges would reverse these changes, especially when reinstating them to their prehistoric distributions. It would partially restore herbivore body mass and diet composition to pre-anthropogenic conditions. However, in the absence of complementary interventions (e.g. introducing functional replacements), many herbivore assemblages would remain down-sized and browser dominated, relative to pre-anthropogenic conditions. Main Conclusions: Many terrestrial herbivore assemblages - and hence ecosystems - would remain trophically downgraded, even after bringing back all extant, native herbivores. Therefore, complementary interventions would be required to achieve complete functional restoration. Nevertheless, our findings suggest that reintroducing the remaining native herbivores would diversify the herbivory and disturbances of herbivore assemblages.

opencc-zeroDec 2021View details →

opencc-by-4.0Jan 2022View details →

LegacyPollen 1.0: A taxonomically harmonized global Late Quaternary pollen dataset of 2831 records with standardized chronologies

This repository consists of code for downloading pollen data from the Neotoma Paleoecology Database, the harmonization of pollen taxa, and the assignment of age-depth data so that datasets for customized harmonization levels can be easily established. The input data includes a harmonization table and example data, stored in machine-readable data format (.CSV).

dryad32/100

Big, flightless, insular, and dead: characterizing the extinct birds of the Quaternary

Aim: Birds have recently undergone a major extinction event which apparently, is ongoing. According to some estimates, humans have caused the extinction of up to 20% of the entire avian species diversity since the latter part of the Pleistocene, which is continuing at an unprecedented rate to this day. Few attempts, however, were made to determine how many extinctions are actually known, rather than projected to have occurred. We aimed to quantify the known avian extinctions, and assess the relevance of factors thought to have promoted their extinctions, i.e., large size, flightlessness, and insularity. Location: Global Taxon: Aves Methods: We collected data on bird extinctions from the literature. We recorded the geographic range, flight ability, and body size of each species. If mass data were unavailable, we estimated it from linear measurements using machine learning tools. We modelled masses of extinct birds on those of extant ones and estimated the effects of taxonomy, body mass, insularity, and flight ability. Results We have identified 469 species of birds that humans, directly or indirectly, drove to extinction. These extinctions have predominantly occurred on islands. Extinct birds were often flightless. We estimated the body mass of 291 extinct species and found that overall, the median mass of extinct species was seven times larger than that of extant ones. Extinctions mostly occurred in families of large-bodied birds, while lineages of small birds have fared better. Insular birds are overall larger than mainland birds, a trend that becomes even more evident when the extinct forms are analyzed. However, within lineages, sizes are only slightly larger on islands than on continents. Main conclusions Our findings suggest that extinct bird species differed from extant birds by being larger, mostly restricted to islands, and often flightless. These factors made them especially vulnerable to human prosecution and to other anthropogenically-related declines. Our modern understanding of birds is skewed with respect to the nature of avian faunas that existed before the current wave of human-induced extinctions changed our world forever.

opencc-zeroMay 2022View details →

opennotspecifiedNov 2017View details →

Distribution. Recorded as living animal from the vicinity of Lake Habbema (3225 m) and an area close to Mt Trikora, WC New Guinea. Late Quaternary subfossils reported (as Hydromys habbema) from Kelangurr Cave and from alluvial terrace of West Baliem River, at 280-2950 m,Papua Province. Tentative record of habbema from a fissure deposit at 3450 m on Mt Jaya requires confirmation. in Muridae

Distribution. Recorded as living animal from the vicinity of Lake Habbema (3225 m) and an area close to Mt Trikora, WC New Guinea. Late Quaternary subfossils reported (as Hydromys habbema) from Kelangurr Cave and from alluvial terrace of West Baliem River, at 280-2950 m,Papua Province. Tentative record of habbema from a fissure deposit at 3450 m on Mt Jaya requires confirmation.

opencc-by-4.0Aug 2022View details →

Thriving in the heat – Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermoactive PEP-synthase

Over time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of Pyrococcus furious, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of P. furiosus. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes. Molecular dynamics simulations and analysis – The all-atom structures of the full c1(X4) 24-mer PPSA models, carrying highly acetylated sites at 14 positions (106, 120,185, 187, 427, 466, 492, 496, 557, 574, 641, 726, 737, 805) or unmodified lysines were coarse grained (CG), mapping their atoms to the SIRAH force field (ff), that uses a classical Hamiltonian common to most all-atom potentials to describe particle–particle interactions, and recently extended to support the PTMs most commonly found on proteins(Garay et al., 2020). Both starting structures contained a disulfide bond between Cys42-Cys189 as well as phosphorylation of Thr440. All starting structures, simulation boxes and parameters files used for the minimization, equilibration and production are provided (Supplementary Data 5). Simulation was conducted in GROMACS 2020.4(Hess et al., 2008), for which code can be found here: <a href="https://doi.org/10.5281/zenodo.5636522">https://doi.org/10.5281/zenodo.5636522</a>. The 24-aly system consisted of 94128 CG atoms for the protein representation, solvated with 179271 WT4 CG water beads (Garay et al., 2020). A neutral charge was achieved adding 6617 NaW (Na+) and 5633 ClW (Cl-), corresponding to a concentration of approximately 150 mM NaCl concentration. The 24-lys system was also prepared accordingly and consisted of 93456 CG atoms for the protein, 186690 WT4 CG water beads and neutralized with 6503 NaW (Na+) and 5855 ClW (Cl-). Solvation was done using the default radii of 0.105 nm for atoms not present in the VdW database (vdwradii.dat) and then removing the WT4 molecules within 0.3 nm from the solute. In all cases, eventual clashes were relaxed during the solute-restrained energy minimization. Due to the length of the loops connecting the 3 domains, an alternative configuration of the tetramers where the CD-NBD domains are sitting on top of the neighboring PPSA subunit is also possible (see Supplementary Note 1). This was named “alternative” (a) configuration, as opposed to the “original” (o), thus producing 4 starting models: a24-aly, o24-aly, a24-lys and o24-lys (Supplementary Data 5). All these configurations were subjected to a first round of production consisting of 125 ns in duplicate to define the stable configuration for further extension of the simulation time to 500 ns. The main stages of the simulation can be summarized as follows:1) solvent and side-chain relaxation by 2 stages of 20’000 steps of energy minimization, imposing positional restraints of 1000 kJ mol-1 nm-2 on the whole protein (stage 1) and only on backbone beads (GN and GO, stage 2); 2) solvent NVT ensemble equilibration with a first stage where the temperature was slowly increased from 303K to 363K in 7 steps of 4 ns each, and a second stage to equilibrate the protein by gradually releasing the positional restraints from 1000 kJ mol-1 nm-2  on the backbone beads (GN and GO) to 100 kJ mol-1 nm-2 on the C-terminus to compensate for the missing stabilization effect of the Met799-Fe cluster; 3) production simulation of an additional 80 ns in NPT ensemble at 363 K and 1 bar imposing positional restraints of 100 kJ mol-1 nm-2 on the C-terminus. Non-bonded interactions were treated with a 1.2 nm cutoff and PME for long-range electrostatics. An integration time-step of 15 fs was used during MD production runs. The system pressure was controlled by the Parrinello-Rahman barostat (Parrinello and Rahman, 1981) with a coupling time of 4 ps. The positional restraints during the production simulation were necessary to maintain the overall system at the high energy of the particles at 363 K (90 ˚C), the temperature mimicking the near-optimum temperature for PPSA catalytic activity. All simulations were run in duplicate. Although the simulations do not accurately reflect the possible dynamics of the protein in native conditions, the computational challenges of simulating >350000 atoms for the protein only drove us to use a CG representation of the system.  To analyze the trajectories, every functional module (tetramer) was extracted from the simulation of the full 24-mer for each replicate, resulting in two sets of 12 independent trajectories (6 for each 24-mer) either with and without acetylated Lysine residues. To produce morphed movies and analyze secondary structure and interfaces, the CG tetramers trajectories were back mapped to atomistic detail using SIRAH tools via VMD. A back mapped atomistic model was produced every 35.7 ns, and subjected to 100 cycles of energy minimization in AMBER, resulting in 14 atomistic models describing each trajectory of a given tetramer over the 500 ns of simulation, further interpolated in ChimeraX using the morph command to produce the atomistic representation of the dynamics (Supplementary Data 5). RMSD calculation and trajectory analysis were done with the MDanalysis suite(Michaud-Agrawal et al., 2011). Each probability density in Figure 5B and 5C is calculated over two independent coarse-grained molecular dynamics simulations of the last 250 ns of production of the PPSA 24-mer in the acetylated and non-acetylated form, using a snapshot frequency of 5 ns. In Figure 5B, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) of the NBD region (residues 1-365) in the tetramer form was calculated with respect to their conformation in the tetramer PPSA resting state. The six trajectories of all six tetramers included in the simulated PPSA complex, resulting in 3 μs ([250ns*6]*2) of accumulated tetramer simulation, were used in the probability density calculation. In Figure 5C, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) was calculated over the CD (residues 379-481) and PBD (residues 510-790) regions with respect to the modelled CD-PBD state of PPSA in the monomer form. All 24 PPSA monomers of which the simulated PPSA complex was composed were included in the probability density calculation, resulting in 12 μs ([250ns*24]*2) of accumulated PPSA monomer simulation.

FIGURE 4 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 4. Plastron and carapace fragments of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a, d, epiplastron fragment (MNHNSD FOS 23.1056), external and internal views; b, e, epiplastron fragment (MNHNSD FOS 23.1060), external and internal views; c, h, costal fragment (NHMUK PV R 36955), internal and external views; f–g, peripheral fragment (MNHNSD FOS 23.1061), external and internal views; i–j, fragment from border of carapacial rim, including two peripherals and part of costal plate (MNHNSD FOS 23.1062), external and internal views. Scale bar=2 cm.

FIGURE 1 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 1. Map of Hispaniola, showing geotectonic boundaries and locations of cave sites from which giant tortoise fossils have been reported. Capital cities indicated with filled stars. Key: 1, Cueva del Papayo; 2, Cueva No. 12; 3, Cueva de las Tortugas; 4, Cueva del Muerto; 5, Cueva de las Caritas; 6, Bayaguana.

FIGURE 3 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 3. Femora of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a–c, MNHNSD FOS 23.1063, left femur (young individual), lateral, anterior and medial views; d–e, MNHNSD FOS 23.1055, right distal femur, anterior and lateral views. Scale bar=2 cm.

FIGURE 2 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 2. Humeri of Chelonoidis marcanoi sp. nov. from Pedernales Province, Dominican Republic: a–b, NHMUK PV R 36954 (holotype), right humerus, anterior and medial views; c–d, MNHNSD FOS 23.1064, left proximal humerus, medial and lateral views; e–f, MNHNSD FOS 23.1058, right humerus, anterior and lateral views; g–h, MNHNSD FOS 23.1054, left humerus, anterior and medial views; i, MNHNSD FOS 23.1059, right distal humerus, anterior view; j–k, MNHNSD FOS 23.1057, left humerus (young individual), anterior and medial views. Scale bar=2 cm.

FIGURE 6 in A new species of extinct Late Quaternary giant tortoise from Hispaniola

FIGURE 6. Schematic drawing of dermal bones of chelonian carapace (left) and plastron (right), indicating approximate estimated position of described shell fragments of Chelonois marcanoi sp. nov. from Pedernales Province, Dominican Republic. Original position on either the left or right side of the carapace is uncertain for the two specimens indicated with asterisks.