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opennotspecifiedJan 2009View details →

Distribution. Grasslands and scrub forest of C South America, from NE Brazil through the Chaco of Paraguay into Rio Grande do Sul State, Brazil, W to Bolivia and Peru border, and S into Uruguay and Argentina to the 30° S parallel. in Canidae

Distribution. Grasslands and scrub forest of C South America, from NE Brazil through the Chaco of Paraguay into Rio Grande do Sul State, Brazil, W to Bolivia and Peru border, and S into Uruguay and Argentina to the 30° S parallel.

opencc-zeroNov 2021View details →

Parallelism in endocarp form sheds light on fruit syndrome evolution in Viburnum

All Viburnum species produce drupes with a hardened endocarp surrounding a single seed. Endocarp form varies greatly within Viburnum, and differences in shape have long been used to distinguish major subclades. Here we trace the evolution of Viburnum endocarp shape using morphometric analyses and phylogenies for 115 Viburnum species. Endocarp measurements were obtained from fruits sampled from herbarium specimens and from field collections, and shapes were analyzed using elliptical Fourier analysis. We infer that the first viburnums had flattened and grooved endocarps. Subsequently, there were multiple losses of grooving in conjunction with shifts to both highly flattened and nearly round endocarps. In several clades the parallel evolution of a derived endocarp shape was accompanied by changes in a suite of other fruit traits, yielding distinctive fruit syndromes likely related to bird dispersal. However, in other clades endocarp shapes similar to the ancestral form have been retained while other fruit traits (color, amount of flesh, nutritional content) have diverged. We quantify cases of parallel evolution in endocarp shape that cut across recognized fruit syndromes such as red, carbohydrate rich fruits with flattened endocarps or blue, lipid rich fruits with round endocarps. Our analyses now invite studies of function and the selective factors that have yielded the distinctive suites of fruit and seed traits that distinguish the major Viburnum lineages.

opennotspecifiedJan 2009View details →

Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40. in Viverridae

Distribution. Angola, DR Congo, Malawi, Mozambique, Tanzania, and Zambia. Description. Head-body 46:5-47-8 cm (males), 44-45-5 cm (females), tail 40-43 cm (males), 38-39 cm (females), hindfoot 8:7-9-8 cm (males), 8-9 cm (females), ear 4-7-5-4 cm (males), 5-1-5-8 cm (females); weight 1-3-2 kg. The coat color is pale ocher, with brownish or grayish tones; melanistic individuals are quite common. The throat and chest are blackish, and the ventral pelage varies from creamy white to dirty white. The stripes and spots on the body vary from different hues of brown to black. The nuchal stripes run as two parallel lines from the nape to the shoulders, where they diverge and enlarge towards the elbows; they are not so conspicuously marked as in other genet species. Below them, a pair of thinner stripes and small spots are scattered on the shoulders and sides of the neck. A third pair of thinner, parallel stripes runs down the neck between the nuchal stripes, extending to about one fourth of the mid-dorsal line, where they vanish or diverge as the first row of flank spots. The black mid-dorsal line is continuous and is flanked on each side by four rows of oblong to squared spots, and by a few small-scattered spots below. There is a dorsal erectile crest. The face has a dark mask and a pair of white sub-ocular spots. The tail has seven to nine black rings, alternating with pale rings; the intervening white spaces are pigmented with a brownish tinge on the dorsal midline. The width of the pale rings relative to the dark rings in the middle of the tail is 50-75%; the tip of the tail is dark. The hindlimbs and forelimbs are black; there are white hairs on the metacarpals and metatarsals. [he posterior parts of the feet are dark. There are two pairs of teats. The posterior chamber of the auditory bulla is not ventrally inflated and has a continuous curve line on the external side. The ratio between the inter-orbital constriction and frontal width is 1-00 + 0-12. Dental formula: 13/3, C1/1,P 4/4, M 2/2 = 40.

opencc-zeroFeb 2022View details →

Phenotype evaluation rawdata of Acinetobacter baumannii harboring chromosomal parallel mutations or an evolved plasmid

OXA-23 is the predominant carbapenemase in carbapenem-resistant Acinetobacter baumannnii. The co-evolutionary dynamics of A. baumannii and OXA-23-encoding plasmids are poorly understood. Here, we transformed A. baumannnii ATCC 17978 with pAZJ221, a blaOXA-23-containing plasmid from a clinical A. baumannnii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time-points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of blaOXA-23 in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3'→5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the causal effects of these mutations on fitness costs and plasmid kinetics, the evolved plasmid containing two copies of blaOXA-23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of blaOXA-23 contributed to host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the unevolved pAZJ221. Overall, our study provides a framework for the co-evolution of A. baumannii and a clinical blaOXA-23-containing plasmid, involving early blaOXA-23 duplication followed by chromosomal adaptations.

opencc-by-4.0Jan 2022View details →

Massively parallel, computationally-guided design of a pro-enzyme

Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects.  While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to re-design any chosen enzyme to be similarly stimulus-responsive.  Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for pro-enzyme design.  As a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity.  Detailed kinetic characterization of most effective designed variants shows that they are inhibited by approximately 80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases.  Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98%, but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing pro-enzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture.  Structural and thermodynamic characterization provides detailed insights into the pro-domain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of pro-proteins with precise spatial regulation.

opencc-by-4.0May 2022View details →

Figures for "The effect of parallel electron plateau on banded chorus generation: 1-D PIC simulations in mirror geometry"

Figures for "The effect of parallel electron plateau on banded chorus generation: 1-D PIC simulations in mirror geometry"

opencc-zeroMay 2022View details →

Data from: Parallel processing in speech perception with local and global representations of linguistic context

Speech processing is highly incremental. It is widely accepted that human listeners continuously use the linguistic context to anticipate upcoming concepts, words, and phonemes. However, previous evidence supports two seemingly contradictory models of how a predictive context is integrated with the bottom-up sensory input: Classic psycholinguistic paradigms suggest a two-stage process, in which acoustic input initially leads to local, context-independent representations, which are then quickly integrated with contextual constraints. This contrasts with the view that the brain constructs a single coherent, unified interpretation of the input, which fully integrates available information across representational hierarchies, and thus uses contextual constraints to modulate even the earliest sensory representations. To distinguish these hypotheses, we tested magnetoencephalography responses to continuous narrative speech for signatures of local and unified predictive models. Results provide evidence that listeners employ both types of models in parallel. Two local context models uniquely predict some part of early neural responses, one based on sublexical phoneme sequences, and one based on the phonemes in the current word alone; at the same time, even early responses to phonemes also reflect a unified model that incorporates sentence-level constraints to predict upcoming phonemes. Neural source localization places the anatomical origins of the different predictive models in nonidentical parts of the superior temporal lobes bilaterally, with the right hemisphere showing a relative preference for more local models. These results suggest that speech processing recruits both local and unified predictive models in parallel, reconciling previous disparate findings. Parallel models might make the perceptual system more robust, facilitate processing of unexpected inputs, and serve a function in language acquisition.

opencc-zeroDec 2021View details →

Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis only in limnetic crosses and breakdown in neither ecotype, suggesting that hybrid incompatibilities are environment-dependent for both ecotypes and that heterosis is environment-dependent in benthic crosses. Heterosis and breakdown were 3× greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, we observed qualitatively similar patterns of heterosis and hybrid breakdown in benthic crosses and limnetic crosses when averaging the lake pairs, suggesting that the outcome of hybridization is repeatable in a general sense.

opencc-zeroJun 2022View details →

Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod

The role of epistasis in adaptive evolution has remained an unresolved problem dating back to the Evolutionary Synthesis. This role is now being revisited due to its relevance for polygenic adaptation. In the absence of epistasis, polygenic adaptation is predicted to result in non-parallel evolution, because repeated selection could act on subsets of effectively redundant alleles. However, positive epistatic interactions among adaptive alleles would make the alleles non-redundant and selection for particular allelic combinations could drive parallel evolution. The inability to address this fundamental question might arise from traditional approaches lacking the power to capture the genomic architecture and dynamics of polygenic adaptation. To address this problem, we employed a replicated and controlled evolution experiment using the copepod Eurytemora affinis to elucidate the evolutionary response architecture to rapid salinity decline, a predicted consequence of global climate change in higher latitudes. Based on time-resolved pooled whole-genome sequencing, we uncovered a remarkably parallel response, despite polygenic adaptation involving over 1000 loci across ten replicate selection lines. Interestingly, single-nucleotide polymorphism (SNP) frequencies converged during the experiment, far beyond expectations, resulting in replicate lines sharing 93.1% of selected alleles. Using simulations, we found that this polygenic parallelism was consistent with synergistic epistasis among alleles responding in concert across replicate lines, a phenomenon that may be common for selection on complex physiological traits. Furthermore, we found that the same SNPs with signatures of selection in the laboratory also exhibited signatures of selection across a natural salinity gradient in the Baltic Sea. Our study provides the first experimental evidence that polygenic adaptation can actually be highly repeatable at the genomic level, given the presence of synergistic epistasis among the loci under selection.

opencc-zeroAug 2022View details →

Data from: Relaxed risk of predation drives parallel evolution of stickleback behaviour

The occurrence of similar phenotypes in multiple independent populations derived from common ancestral conditions (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviours between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioural traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that divergence in behaviour between habitats is aligned with the response to relaxation of predation pressure. Finally, we show alignment across multiple pairs of populations, and that relaxation of predation pressure has likely driven parallel evolution of behaviour in this species.

Figure 16 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 16. Macrobiotus kirghizicus from the Kyrgyz Republic – the oral cavity armature seen in SEM: A, dorsal view on the oral cavity armature; B, ventral view on the oral cavity armature; C, details of the first band of teeth. Filled indented arrowheads indicate the first band of teeth in the

Figure 17 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 17. Macrobiotus kirghizicus from the Kyrgyz Republic – egg chorion morphology seen in PCM: A, B, egg surface under 1000× magnification; C–F, egg processes midsections under 1000× magnification. Filled flat arrowheads indicate pores within the basal portion of egg processes wall, indented empty arrowheads indicate short dark thickenings around the process bases below or at the same level as the lower ring of pores, empty flat arrowheads indicate septum between the basal and distal portion of egg process. Scale bars in µm.

Figure 19 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 19. Bayesian phylogenetic reconstruction of Superclade I of the family Macrobiotidae. Values at nodes are BI posterior probability supports, with maximum values (1.00) indicated by asterisks (*). Newly sequenced and/or newly analysed taxa/populations are bolded. Taxa exhibiting claws of typical size and proportions are presented in black font,

Figure 14 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 14. Macrobiotus kirghizicus from the Kyrgyz Republic – claws (paratypes): A, B, claws II and IV seen in PCM, respectively; C, single continuous cuticular bar and double muscle attachments on leg III seen in PCM; D, E, claws II and IV seen in SEM, respectively. Empty flat arrowheads indicate accessory points, filled flat arrowheads indicate double muscles attachments under the claws, filled indented arrowhead indicates cuticular bar. Scale bars in µm.

Figure 12 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 12. Macrobiotus kirghizicus from the Kyrgyz Republic: A, habitus, dorsoventral projection (Hoyer's medium, PCM); B, C, cuticular pores on the dorsocaudal part of the body seen in PCM and SEM, respectively. Filled flat arrowheads indicate faint body granulation. Scale bars in µm.

Figure 11 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 11. Macrobiotus ariekammensis groenlandicus subsp. nov. – egg chorion morphology seen in SEM: A, entire egg; B, magnification of the egg surface; C, D, details of the egg processes; E, F, details of the terminal portion of egg processes. Filled flat arrowheads indicate pores within the basal portion of the process wall. Scale bars in µm.

Figure 9 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 9. Macrobiotus ariekammensis groenlandicus subsp. nov. – buccal apparatus and oral cavity armature seen in SEM: A, entire buccal apparatus; B, ventral view of the buccal crown; C, D, placoids morphology; E, magnification of the middle part of the buccal apparatus with stylet support insertion points; F, the oral cavity armature. Filled arrows indicate two globular protuberances on the ventral side of the buccal crown and buccal tube, empty arrows indicate dorsal cuticular spikes, empty indented arrowheads indicate central constrictions in first macroplacoid and subterminal constriction in second macroplacoid, filled flat arrowhead indicates a single tooth in dorsal portion of the third band of teeth in the oral cavity. Scale bars in µm.

Figure 8 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 8. Macrobiotus ariekammensis groenlandicus subsp. nov. – buccal apparatus and the oral cavity armature seen in PCM: A, dorsoventral projection of the entire buccal apparatus; B, C, oral cavity armature visible from dorsal (B) and ventral (C) view, respectively; D, oral cavity armature visible from lateral view; E, macroplacoid morphology. Filled flat arrowheads indicate a single tooth in dorsal portion of the third band of teeth in the oral cavity, empty arrows indicate dorsal cuticular spikes, empty indented arrowheads indicate central constrictions in first macroplacoids and subterminal constriction in second macroplacoid. Scale bars in µm.

Figure 13 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 13. Macrobiotus kirghizicus from the Kyrgyz Republic – cuticular structures on legs: A, B, granulation on the external surface of legs III seen in PCM (A) and SEM (B), respectively; C, D, granulation on the internal surface of legs III and II seen in PCM (C) and SEM (D), respectively; E–F, granulation on the dorsal and dorsolateral surface of leg IV seen

Figure 10 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 10. Macrobiotus ariekammensis groenlandicus subsp. nov. – egg chorion morphology seen in PCM: A–D, egg surface under 1000× magnification; E–P, egg processes midsections under 1000× magnification. Filled flat arrowheads indicate a crown of dark thickenings and pores arranged alternately around egg process bases, filled indented arrowheads indicate light-refracting dots in the egg surface between the processes, empty flat arrowheads indicate septum between the basal and distal portion of egg process. Scale bars in µm.