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Morphological characteristics of pollen from triploid watermelon and its fate on stigmas in a hybrid crop production system
<p>Hybrid crop production is more reliant on pollinators compared to open-pollinated crops because they require cross-pollination between a male-fertile and a male-sterile line. Little is known about how stigma receipt of pollen from male-sterile genotypes affects reproduction in hybrids. Non-viable and non-compatible pollen cannot fertilise plant ovules, but may still interfere with pollination success. Here we used seedless watermelon (<em>Citrullus lanatus</em> (Thunb.) Matsum. & Nakai) as a model hybrid plant, to evaluate the morphology, physiology, and movement of pollen from inter-planted genotypes (diploids and triploids). We found that pollen from triploids ('Exclamation' and 'Royal Armada') and diploids ('SP-6', 'Summer Flavor 800', and 'Tiger') was visually distinguishable. Pollen in triploids had more deformities (42.4–46%), tetrads (43–44%), and abnormal growth of callose plugs in pollen tubes. The amount of pollen in triploids to germinate on stigmas was low (8 ± 3%), and few pollen grains produced pollen tubes (6.5 ± 2%). Still, contrary to previous reports our results suggest that some viable pollen grains are produced by triploid watermelons. However, whilst honey bees can collect and deposit pollen from triploids onto stigmas, its effect on hybrid watermelon reproduction is likely to be minimal due to its low germination rate.</p>
Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times
<p><span><span><span><span><span><span><span><span><span><span><span>Natural hybrid zones have provided important insights into the evolutionary process, and their geographic dynamics over time can help to disentangle the underlying biological processes that maintain them. Here, we leverage replicated sampling of an identical transect across the hybrid zone between yellow-shafted and red-shafted flickers in the Great Plains to assess its stability over ~60 years (1955-1957 to 2016-2018). We identify a ~73 km westward shift in the hybrid zone center towards the range of the red-shafted flicker, but find no associated changes in width over our sampling period. In fact, the hybrid zone remains remarkably narrow, suggesting some kind of selective pressure maintains the zone. By comparing to previous work in the same geographic region, it appears likely that the movement in the hybrid zone has occurred in the years since the early 1980s. This recent movement may be related to changes in climate or land management practices that have allowed asymmetric westward movement of yellow-shafted flickers into the Great Plains.</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 3. A–C in A new putative natural hybrid of Cyrtopodium (Orchidaceae) from the south coast of Brazil
FIGURE 3. A–C. Cyrtopodium × intermedium (A, Batista & Alan 2702—BHCB; B, Batista 3030—BHCB; C, Batista & Alan 2700 – BHCB; all from Rio de Janeiro). D–E. Cyrtopodium glutiniferum (Batista & Alan 2703—BHCB, Rio de Janeiro). F. Cyrtopodium gigas (Batista & Alan 2701—BHCB, Rio de Janeiro).
FIGURE 2 in A new putative natural hybrid of Cyrtopodium (Orchidaceae) from the south coast of Brazil
FIGURE 2. Cyrtopodium × flavopunctatum. A. Habit and inflorescence. B. Flower, front view. C. Perianth. D. Bract. E. Ovary and gynostemium. Drawn by Alexandre Medeiros from Medeiros 1179.
FIGURE 1 in A new putative natural hybrid of Cyrtopodium (Orchidaceae) from the south coast of Brazil
FIGURE 1. Habitat and morphological characters of Cyrtopodium × flavopunctatum. A. Habitat, shrubby resting in sandy coastal plain, municipality of São Francisco do Sul, state of Santa Catarina. B. Cyrtopodium plants in the locality of the type. C. Inflorescence. D. Flower, front view E. Flower, dissected segments. Putative parental species. F. Cyrtopodium flavum (without voucher, São Francisco do Sul, Santa Catarina). G. Cyrtopodium gigas (Batista 1448—CEN, Santa Catarina). H. Cyrtopodium palmifrons (without voucher, Minas Gerais). Scale bars: C = 5 cm; D–E = 1 cm.
Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA
<p>The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains (Mathieson et al., 2015; Narasimhan et al., 2019) or sediments (Vernot et al., 2021; Wang et al., 2021; Zavala et al., 2021) in single studies. Yet demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here we explore the possibility of improving the economics of sample preparation via multiplex capture, i.e. the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible for small genomic targets, such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the re-amplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination. </p>
Quantum Properties in Hybrid Nanowire Devices
<p>The raw data and the data analysis codes that support the findings of the chapters 7 and 8 of the doctoral dissertation titled "Quantum Properties in Hybrid Nanowire Devices".</p> <p>A digital copy of the dissertation can be found via the doi: <a href="https://doi.org/10.4233/uuid:26c9e59f-5d64-40a4-adb9-cabe2c272bcb">https://doi.org/10.4233/uuid:26c9e59f-5d64-40a4-adb9-cabe2c272bcb</a>.</p> <p>The research was conducted at QuTech, Delft University of Technology, under the supervision of Leo Kouwenhoven.</p>
Processes underlying complex patterns of song trait evolution in a Setophaga hybrid zone
During secondary contact between two species when hybrids are less fit than parents, mating signals are expected to diverge while aggressive signals are expected to converge. If a single signal trait is used in both mating and aggression, then the dynamics between these two forces could influence the evolutionary trajectory of that trait. We studied such a situation in an avian hybrid zone between two Setophaga species, where birdsong is used in both mate attraction and territory defense. We hypothesized that song modules of the two species will show separate and distinct geographic patterns due to the influence of selective pressures for effective territorial aggression and for effective mate attraction. We conducted geographic cline analyses and playback experiments across this hybrid zone. We found an unexpected geographical pattern of asymmetric introgression of song rhythm, which may be explained by results of the playback experiments that suggest that differences in song rhythm serve a greater role in mate attraction than in territory defense. In contrast, differences in syllable morphology show little evidence of importance in mate attraction or territorial defense. Song features converge in the hybrid zone, yet patterns of trait change suggest that the song production modules may vary in their modes of development and inheritance. Syringeal motor gesturing, which gives rise to syllable morphology, shows a non-clinal mosaic pattern, suggesting that this trait may be predominantly learned. In contrast, respiratory patterning, which forms song rhythm, shows a clinal geographic transition, suggesting that this trait could be more innate. The results indicate that opposing forces act independently on song via distinct modules of the song production mechanism, driving complex patterns of song trait evolution.
FIGURE 1 in Typification of the names Verbascum limnense and Celsia tomentosa (Scrophulariaceae) and a new nothospecies, V. × sipiadense, with the hybrid formula V. limnense × V. sinuatum
FIGURE 1. Neotype of Verbascum limnense Fraas mounted on two sheets, kept in UPA (UPA-33037, UPA-33038)
Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme
<p>This repository contains the results of 2D simulations of the earthquake cycles accounting for off-fault plasticity.</p> <p>Folder Case1 contains the slip rate and time history for all simulations with cohesion c = 47 MPa</p> <p>Folder Case2 contains the slip rate and time history for all simulations with cohesion c = 25 MPa</p> <p>the mat files contain equivalent plastic strain of each element stored at the start and end of each event with element connectivity and node coordinates.</p>
Figure 3 in Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization
Figure 3. Discriminant analysis of principal component (DAPC) plot of SNP variation amongst Australian mussels with the inclusion of reference Northern and Southern hemisphere populations of Mytilus spp. sampling groups: (1) M. galloprovincialis, (2) Mytilus spp.: samples from New Zealand mainland with some Australian individuals, mainly from Port Arthur, Tasmania, (3) M. platensis, (4) M. chilensis, (5) M. edulis, (6) M. galloprovincialis × M. planulatus hybrids from Australia and (7) New Zealand offshore island samples (AUCB and CAMI). For details of group membership refer to Supporting Information, Table S6.
Figure 2 in Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization
Figure 2. Neighbour joining (NJ) tree of the ten mussel samples from Australia, three from New Zealand and reference samples of Mytilus galloprovincialis, M. edulis, M. platensis, M. chilensis and M. trossulus, based on the FST matrix from allele frequencies of the SNP loci. NJ tree obtained with POPTREEW and visualized with MEGA v.6. Population/sample codes as shown in Table 1. For the Australian samples: -W, wild; -F, farmed. FST matrix details are presented in Supporting Information, Table S5.
Figure 7 in Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization
Figure 7. Structure plot (K = 3) for Australian 'pure' native Mytilus planulatus pooled as one group (Austr.), two reference Northern hemisphere M. galloprovincialis samples (CAM, ORI), mainland New Zealand (AKAR) and offshore island lineages (AUCB, CAMI) of M. aoteanus. Plots constructed based on Australian individuals without admixture, identified by STRUCTURE and assigned to the M. planulatus cluster (q> 0.8). Each individual is represented by a single vertical line, samples are separated by a black vertical line, and site abbreviations (Table 1) are given along with reference taxon names.
Figure 4 in Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization
Figure 4. Discriminant analysis of principal component (DAPC) plot of SNP variation amongst Australian mussels with the inclusion of reference Northern and Southern hemisphere populations of Mytilus spp. Sampling groups: (1) New Zealand mainland with some Australian individuals, mainly from Port Arthur, Tasmania, (2) reference M. galloprovincialis from the Mediterranean Sea and the North Atlantic Ocean with some Australian individuals, (3) New Zealand offshore island samples, (4) mixed status mussels from Australia (individuals from all ten sampled Australian sites) and some reference M. galloprovincialis from the Mediterranean Sea. For details of group membership refer to Supporting Information, Table S7.
Figure 1 in Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization
Figure 1. Geographic locations of ten mussel sampling sites in Australia. See Table 1 for details of site codes, numbers of individuals per location, and origin: -W, wild; -F, farmed mussels.
Data from: Population genomic evidence of selection on structural variants in a natural hybrid zone
<p><span>Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two </span><em>Lycaeides</em> butterfly taxa (<em>L. melissa</em> and Jackson Hole <em>Lycaeides</em>) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole <em>Lycaeides</em> ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole <em>Lycaeides</em>. Excess Jackson Hole <em>Lycaeides</em> ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.</p>
FIGURE 1 in Urospermum ×siljakii (Asteraceae), a new natural homoploid hybrid between U. dalechampii and U. picroides
FIGURE 1. Urospermum ×siljakii (B, E, H) and its parental species: U. dalechampii (A, D, G) and U. picroides (C, F, I). Frontal views of capitula (A−C), details of the involucre indumentum (D−F), and plants growing in habitat (G−I). Scale bars: 1 cm. Photographs: Oriane Hidalgo (material: U. dalechampii, OH 668, BC; U. ×siljakii, OH 652 & OH 666, BC; U. picroides, OH 651, BC).
On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages
<p>C<sub>2</sub> photosynthesis is characterized by recapturing photorespiratory CO<sub>2</sub> by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C<sub>3</sub> and C<sub>4</sub> photosynthesis. C<sub>2</sub> can be interpreted as an evolutionary precursor of C<sub>4</sub> and/or as the result of hybridization between a C<sub>3</sub> and C<sub>4</sub> lineage.</p> <p>We compared the expression of photosynthetic traits among populations of the <em>Salsola divaricata </em>agg. (C<sub>2</sub>) from humid subtropical to arid habitats on the coasts of the Canary Islands and Morocco and subjected them to salt and drought treatments. We screened for enhanced C<sub>4</sub>-like expression of traits related to habitat or treatment. We estimated species trees with a transcriptome dataset of Salsoleae and explored patterns of gene tree discordance. With phylogenetic networks and hybridization analyses we tested for hybrid origin of the <em>Salsola divaricata </em>agg.</p> <p>We observed distinct independent variation of photosynthetic traits within and among populations and no clear evidence for selection towards C<sub>4</sub>-like trait expression in more stressful habitats or treatments. We found reticulation and gene tree incongruence in Salsoleae supporting a putative hybrid origin of the <em>Salsola divaricata </em>agg.</p> <p>C<sub>2</sub> photosynthesis in the <em>Salsola divaricata </em>agg. combines traits inherited from its C<sub>3</sub> and C<sub>4</sub> parental lineages and seems evolutionarily stable, possibly well adapted to a wide climatic amplitude.</p>
Subspecies and Distribution. A.l.lerviaPallas,1777—Morocco,NA.l.,andNTunisia. A.l.angusiRothschild,1921—NWNiger(Air&TermitMassifs). A.l.blaineiRothschild,1913—SELybia,NEChad,andNW&NESudan(probablynowrestrictedtoRedSeahills). A.l.fassiniLepri,1930—NWLibya,extremeSTunisia. A.l.ornatus1.GeoffroySaint-Hilaire,1827—SE&SWEgypt. A. l. sahariensis Rothschild, 1913 — S Morocco, Western Sahara, NW Mauritania, S A.l ria, extreme S Libya, NE Mali, SE Niger, and NW Chad. Introduced, free-ranging populations occur in S Spain, the Canary Is, USA (California, New Mexico, and Texas), and NE Mexico. Subspecies of free-ranging introduced populations are unknown because they originate from zoo animals of uncertain origin or from hybrids. Most introduced populations are probably from subspecies lervia, derived from European zoos. The Aoudad has become a widespread invasive species. in Bovidae
Subspecies and Distribution. A.l.lerviaPallas,1777—Morocco,NA.l.,andNTunisia. A.l.angusiRothschild,1921—NWNiger(Air&TermitMassifs). A.l.blaineiRothschild,1913—SELybia,NEChad,andNW&NESudan(probablynowrestrictedtoRedSeahills). A.l.fassiniLepri,1930—NWLibya,extremeSTunisia. A.l.ornatus1.GeoffroySaint-Hilaire,1827—SE&SWEgypt. A. l. sahariensis Rothschild, 1913 — S Morocco, Western Sahara, NW Mauritania, S A.l ria, extreme S Libya, NE Mali, SE Niger, and NW Chad. Introduced, free-ranging populations occur in S Spain, the Canary Is, USA (California, New Mexico, and Texas), and NE Mexico. Subspecies of free-ranging introduced populations are unknown because they originate from zoo animals of uncertain origin or from hybrids. Most introduced populations are probably from subspecies lervia, derived from European zoos. The Aoudad has become a widespread invasive species.
Do habitat and elevation promote hybridization during secondary contact between three genetically distinct groups of warbling vireo (Vireo gilvus)?
<p>Following postglacial expansion, secondary contact can occur between genetically distinct lineages. These genetic lineages may be associated with specific habitat or environmental variables and therefore, their distributions in secondary contact could reflect such conditions within these areas. Here we used mtDNA, microsatellite, and morphological data to study three genetically distinct groups of warbling vireo (Vireo gilvus) and investigate the role that elevation and habitat play in their distributions. We studied two main contact zones and within each contact zone, we examined two separate transects. Across the Great Plains contact zone, we found that hybridization between eastern and western groups occurs along a habitat and elevational gradient, whereas hybridization across the Rocky Mountain contact zone was not as closely associated with habitat or elevation. Hybrids in the Great Plains contact zone were more common in transitional areas between deciduous and mixed-wood forests, and at lower elevations (<1000 m). Hybridization patterns were similar along both Great Plains transects indicating that habitat and elevation play a role in hybridization between distinct eastern and western genetic groups. The observed patterns suggest adaptation to different habitats, perhaps originating during isolation in multiple Pleistocene refugia, is facilitating hybridization in areas where habitat types overlap.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.