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Figure 4 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 4. Asphondylia cipo sp. nov. (A, B) Pupa in ventral view; (C) Posterior region of pupa in dorsal view; (D) Prothoracic spiracle and the accessory structure.

Figure 1 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 1. Asphondylia cipo sp. nov.(A) Head in frontal view;(B) Male 3rd flagellomere;(C) Female 3rd flagellomere; (D) Male 9th-12th flagellomeres; (E) Female 9th-12th flagellomeres;(F) Palpus; (G) First tarsomere with apicoventral spur; (H) Foretarsal claw and empodium; (I) Midtarsal claw and empodium;(J) Foretarsal claw and empodium.

Figure 8 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 8. Terminal segment of Asphondylia species. (A) Asphondylia glomerata, (B) A. ajjalai, (C) A. salvadorensis, (D) A. ulei, (E) A. gochnatiae, (F) A. serrata. Figure 8A modified from Gagné et al. (2001), 8B, 8C from Möhn (1959), 8D from Möhn (1973), 8E from Maia (2004).

Figure 6 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 6. Stem and petiole galls induced by Asphondylia cipo sp. nov. in Lessingianthus warmingianus (Baker) H. Rob. (Asteraceae). Arrow indicates a petiole gall.

Figure 3 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 3. Asphondylia cipo sp. nov. (A, B) Abdominal segments 7 and 8 and ovipositor in ventro-lateral view. Abbreviation: cl = cercilike lobes.

Figure 2 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 2. Asphondylia cipo sp. nov. (A, B) Male abdomen in lateral view; (C, D) Male terminalia in dorsal view. Abbreviations: ce = cercus, gc = gonocoxite, gs = gonostyle, hy = hypoproct, s7 = sternite 7, th = teeth of gonostyle.

Figure 5 in A new species of Asphondylia (Diptera: Cecidomyiidae) and a key to separate species of the genus associated with Asteraceae from Neotropical region

Figure 5. Asphondylia cipo sp. nov. (A) Larval spatula and lateral papillae in ventral view; (B) Larval eighth and terminal segment with terminal papillae, in dorsal

opencc-by-4.0Oct 2021View details →

Derivative products: "IBEX Ribbon Separation Using Spherical Harmonic Decomposition of the Globally Distributed Flux" by Swaczyna et al.

Derivative products from: Swaczyna et al. 2022, "IBEX Ribbon Separation Using Spherical Harmonic Decomposition of the Globally Distributed Flux", ApJS, 258:6

opencc-by-4.0Oct 2022View details →

Data for "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics"

We provide the raw data for the paper "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics". The files hold time tagged and time resolved single photon data from experiments on immobilized structures as well on free diffusion structures. The files have PicoQuant's .ptu files-format. Additionally we provide the python scripts used to analyze these data sets.

opencc-zeroJan 2023View details →

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

The accurate delimitation of species boundaries in non-bilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondria]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi colour morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.

opencc-zeroFeb 2023View details →

Data from: Separate and combined effects of boat noise and a live crab predator on mussel valve gape behaviour

Data abstract: Data on the valve gape of mussels and the behaviour of stimulus crabs during sound exposure trials. We provide the raw valve gape data, processed data, and scripts to process the raw data, make plots, and run the statistics. Paper abstract: Noisy human activities at sea are changing the acoustic environment, which has been shown to affect marine mammals and fishes. Invertebrates, such as bivalves, have so far received limited attention despite their important role in the marine ecosystem. Several studies have examined the impact of sound on anti-predator behaviour using simulated predators, but studies using live predators are scarce. In the current study, we examined the separate and combined effects of boat sound playback and predator cues from shore crabs (Carcinus maenas) on the behaviour of mussels (Mytilus spp.). We examined the behaviour of the mussels using a valve gape monitor and scored the behaviour from the crabs in one of two types of predator test conditions from video footage to control for effects from potential, sound-induced variation in crab behaviour. We found that mussels closed their valve gape during boat noise and with a crab in their tank, but also that the stimulus combination did not add up to an even smaller valve gape. The sound treatment did not affect the stimulus crabs, but the behaviour of the crabs did affect the valve gape of the mussels. Future research is needed to examine whether these results stand in situ and whether valve closure due to sound have fitness consequences for mussels. The effects on the well-being of individual mussels from anthropogenic noise may be relevant for population dynamics in the context of pressure from other stressors, their role as ecosystem engineers, and in the context of aquaculture.

opencc-by-4.0Mar 2023View details →

HairSplitter: separating strains in metagenome assemblies with long reads

Datasets, command lines and assemblies analyzed in the manuscript "HairSplitter: separating strains in metagenome assemblies with long reads".

opencc-zeroMar 2023View details →

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

opencc-by-4.0Aug 2022View details →

Data underpinning "Disorder-induced spin-charge separation in the 1-D Hubbard model"

Many-body localisation is believed to be generically unstable in quantum systems with continuous non-Abelian symmetries, even in the presence of strong disorder. Breaking these symmetries can stabilise the localised phase, leading to the emergence of an extensive number of quasi-locally conserved quantities known as local integrals of motion, or l-bits. Using a sophisticated non-perturbative technique based on continuous unitary transforms, we investigate the one-dimensional Hubbard model subject to both spin and charge disorder, compute the associated l-bits and demonstrate that the disorder gives rise to a novel form of spin-charge separation. We examine the role of symmetries in delocalising the spin and charge degrees of freedom, and show that while symmetries generally lead to delocalisation through multi-particle resonant processes, certain subsets of states appear stable.

opencc-by-4.0Dec 2015View details →

Fig. 1 in An annotated key separating foreign earthworm species from the indigenous South African taxa (Oligochaeta: Acanthodrilidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Microchaetidae, Ocnerodrilidae and Tritogeniidae)

Fig. 1. (A) Acanthodriline arrangement (schematic); (B) Parachilota timothyi (Acanthodrilinae).

opencc-by-4.0Dec 2015View details →

Fig. 7 in An annotated key separating foreign earthworm species from the indigenous South African taxa (Oligochaeta: Acanthodrilidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Microchaetidae, Ocnerodrilidae and Tritogeniidae)

Fig. 7. Prostomium: (A) zygolobous; (B) prolobous; (C) epilobous; (D) tanylobous.

opencc-by-4.0Dec 2015View details →

Fig. 2 in An annotated key separating foreign earthworm species from the indigenous South African taxa (Oligochaeta: Acanthodrilidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Microchaetidae, Ocnerodrilidae and Tritogeniidae)

Fig. 2. (A) Balantine arrangement (schematic); (B) Udeina quedeni (Acanthodrilinae).

opencc-zeroMay 2023View details →

Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low

Genetic divergence among isolated populations is not always reflected in phenotypic differentiation. We investigated the genetic and phenotypic differentiation in Diglossa cyanea (Thraupidae; Masked Flowerpiercer), a widely distributed species in the tropical Andes. We found strong evidence for two main lineages separated by the Marañón River valley in the Northern Peruvian Low (NPL). These two lineages show a deep sequence divergence in mitochondrial DNA (mtDNA; ~6.7% uncorrected p-distance, n = 122), spectral frequency and song structure (with exclusive final whistles in southern populations, n = 88), and wing length (the northern populations are smaller, n = 364). The two divergent D. cyanea mitochondrial lineages were not sister to each other, suggesting a possible paraphyly with respect to D. caerulescens (Bluish Flowerpiercer) that remains to be tested with nuclear genomic data. No genetic variation, size difference or song structure was observed within the extensive range of the southern group (from the NPL to central Bolivia) or within all sampled northern populations (from the NPL to Venezuela). These vocal differences appear to have consequences for song discrimination, and species recognition, according to a previously published playback experiment study. We propose that the southern taxon be elevated to species rank as D. melanopis, a monotypic species (with the proposed name Whistling Masked-Flowerpiercer). In turn, we provide a redefinition of D. cyanea (Warbling Masked-Flowerpiercer), which is now restricted to the northern half of the tropical Andes as a polytypic species with three subspecies (tovarensis, obscura, and cyanea). Based on our results, the subspecies dispar should be treated as a junior synonym of cyanea. Our study highlights the need to continue amassing complementary datasets from field observations, experiments, and collection-based assessments to better characterize the evolutionary history, biogeography, bioacoustics, and taxonomy of Neotropical montane birds.

opencc-zeroJun 2023View details →

Data and code for: Optimal clutch size revisited: separating individual quality from the costs of reproduction

Life-history theory, central to our understanding of diversity in morphology, behaviour and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness – reproduction and survival – questioning the theory's general validity. We used a meta-analysis to separate quality effects from the costs of reproduction using studies of parental investment and survival in birds. Experimental enlargement of broods caused reduced parental survival. However, the effect of experimental enlargements was small and opposite to the effect of phenotypic quality, where individuals that naturally produced larger clutches also survived better. The opposite effects on survival in experimental and observational studies of parental care provide the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproduction and longevity, operating within a population. We suggest that within species, the fitness landscape of the reproduction–survival trade-off is flat until it reaches the boundaries of the between-species fast-slow life-history continuum. Our interpretation explains why the costs of reproduction are not apparent and why variation in reproductive output persists within species.