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dryad32/100

Data from: The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site–leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna

Background. Ecosystem Engineers are species that transform habitats in ways that influence other species. While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods. We conducted our research in South America's Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results. We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes is consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion. Atta laevigata in the Cerrado modify local conditions in ways that have strong but spatially restricted consequences for plant communities. We hypothesize that ants indirectly reduce seedling establishment by clearing litter and reducing soil moisture, which leads to seed and seedling desiccation. Altering soil nutrients could also reduce juvenile growth and survivorship; if so these indirect negative effects of engineering could exacerbate their direct effects of harvesting plants. The effects of Atta appear restricted to nest mounds, but they could be long-lasting because mounds persist long after a colony has died or migrated. Our results support the hypothesis that leaf-cutter ants play a dominant role in Cerrado plant demography. We suggest the ecological and economic footprint of these engineers may increase dramatically in coming decades due to the transformation of the Cerrado by human activities.

opencc-zeroDec 2017View details →
dryad32/100

Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic

Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site associated DNA sequencing (RAD-seq), microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Concerted versus independent evolution and the search for multiple refugia: comparative phylogeography of four forest beetles

Phylogeographic structure and its underlying causes are not necessarily shared among community members, with important implications for using individual organisms as indicators for ecosystem evolution, such as the identification of forest refugia. We used mitochondrial DNA (COI), Bayesian coalescent ancestral state reconstruction (implemented in BEAST) and ecological niche models (ENMs) to construct geo-spatial histories for four co-distributed New Zealand forest beetles (Leiodidae, Nitidulidae, Staphylinidae, Zopheridae) to examine the extent to which they have tracked environmental changes together through time. Hindcast ENMs identified potential forest refugia during the Last Glacial Maximum, while ancestral state reconstruction identified key geographic connections for each species, facilitating direct comparison of dispersal patterns supported by the data and the time frame in which they occurred. Well-supported geographic state transitions for each species were mostly between neighboring regions, favoring a historical scenario of stepping stone colonization of newly-suitable habitat rather than long distance dispersal. No geographic state transitions were shared by all four species, but three shared multiple projected South Island refugia and recent dispersal from the southernmost refugium. In contrast, strongly supported dispersal patterns in the refugia-rich northern South Island suggest more individualistic responses to environmental change in these ecologically similar forest species.

opencc-zeroDec 2010View details →
dryad32/100

Data from: Separating sources of density-dependent and density-independent establishment limitation in invading species

Successful colonization by invasive species depends on both the ability to disperse seeds to a site and an ability to establish once seeds have arrived. While seed and establishment limitation are known to jointly influence colonization, decomposing establishment limitation into density-dependent and density-independent components has remained challenging. Here, we couple theoretical models of recruitment with a multispecies invasion experiment conducted within a natural gradient of soil moisture and productivity to assess how variation in establishment limitation shapes outcomes for invasion. Recruitment was affected by both density-dependent and density-independent sources of establishment limitation in three of four species. Soil moisture stress and productivity both increased density-independent mortality in one species, whereas density-dependent mortality increased in locations with favourable soil moisture. Synthesis. Successful establishment of invading species can be limited by both density-dependent and density-independent mechanisms. In particular, the strength of density-independent limitation may depend on natural gradients in abiotic factors. The varying strengths of establishment limitation suggest that patterns of invasion are likely to be uneven both in space and in time. Understanding how intraspecific competitive constraints and density-independent limitation vary with abiotic gradients can assist with predicting when invasions are likely to occur, information that can be harnessed in the development of better methods for control.

opencc-zeroDec 2015View details →
dryad32/100

Data from: Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages.

opencc-zeroDec 2016View details →
dryad32/100

Data from: A key floral scent component (β-trans-bergamotene) drives pollinator preferences independently of pollen rewards in seep monkeyflower

1) Floral odors play an important role in attracting insect pollinators. Because pollinators visit flowers to obtain pollen and nectar rewards, they should prefer floral odor profiles associated with the highest-rewarding flowers (honest signals). In previous work, bumble bees exhibited a preference for flowers from outbred over inbred Mimulus guttatus plants. Pollen is the only floral reward in M. guttatus, and pollen viability (a reliable indicator of protein content) is reduced in inbred plants. Yet, differences in pollen viability did not explain the observed preferences. 2) In this study we examined the floral volatile profiles of inbred and outbred M. guttatus to identify inbreeding effects and associations between volatile compounds and the number of viable pollen grains per flower, designated 'PRQ' (pollen reward quality). We also conducted pairwise choice tests with Bombus impatiens to evaluate the ability of bees to discriminate between odors of rewarding and nonrewarding flowers and to determine whether bumble bee preferences are explained by differences in the floral odors of inbred and outbred plants. 3) Inbred plants exhibited reduced emission of β-trans-bergamotene, the second-most abundant compound in the volatile blend of outbred plants. Furthermore, pollen and fertile anthers emitted nonadecane. Six other compounds in the floral blend were positively correlated with PRQ. There was no overlap between compounds affected by inbreeding and compounds associated with PRQ. 4) Even when given prior experience foraging on M. guttatus, bumble bees did not distinguish between the floral odors of rewarding and non-rewarding outbred plants. However, they preferred floral odors from non-rewarding outbred plants over rewarding inbred plants. Bumble bees without prior experience of flowers preferred volatile blends with higher versus lower amounts of β-trans-bergamotene. 5) Taken together, these results suggest that the volatile emissions of M. guttatus provide reliable indicators of pollen rewards (potential honest signals), but that the preference of bumble bees for outbred plants is not driven by these cues but rather by a sensory bias for β-trans-bergamotene. This may represent a subtle form of deceit-pollination that allows plants to attract pollinators while minimizing investment in costly rewards.

opencc-zeroDec 2017View details →
dryad32/100

Data from: Survival to independence in relation to pre-fledging development and latitude in songbirds across the globe

Species differ strongly in their life histories, including the probability of survival. Annual adult survival was investigated extensively in the past, whereas juvenile survival, and especially survival to independence, received much less attention. Yet, they are critical for our understanding of population demography and life-history evolution. We investigated post-fledging survival to independence (i.e. survival upon leaving the nest until nutritional independence) in 74 species of passerine birds worldwide based on 100 population level estimates extracted from published literature. Our comparative analyses revealed that survival to independence increased with the length of nestling period and relative fledging mass (ratio of fledging mass to adult body mass). At the same time, species with higher nest predation rates had shorter nestling periods and lower relative fledging mass. Thus, we identify an important trade-off in life history strategies: staying longer in the nest may improve post-fledging survival due to enhanced flight ability and sensory functions, but at the cost of a longer exposure to nest predators and increased mortality due to nest predation. Additionally, post-fledging survival to independence did not differ between species from the northern temperate zone vs species from the tropics and southern hemisphere. However, analyses of post-fledging survival curves suggest that 1) daily survival rates are not constant and improve quickly upon leaving the nest, and 2) species in the tropics and southern hemisphere have higher daily post-fledging survival rates than northern temperate species. Nevertheless, due to the accumulation of mortality risk during their much longer periods of post-fledging care, overall survival until independence is comparable across latitudes. Obtaining high-quality demographic data across latitudes to evaluate the generality of these findings and mechanisms underlying them should be a research priority.

opencc-zeroDec 2015View details →
dryad32/100

Data from: Post‐independence mortality of juveniles is driven by anthropogenic hazards for two passerines in an urban landscape

Urban environments impose novel selection pressures with varying impacts across species and life history stages. The post‐fledging stage for migratory passerines, defined as the period of time from when hatch‐year birds fledge until their first migration, is a poorly understood component of annual productivity that potentially limits population growth. We studied two migratory passerines with positive and negative population responses to urbanization, respectively: Gray Catbird (Dumetella carolinensis) and Wood Thrush (Hylocichla mustelina). Our goals were to estimate post‐fledging survival rates for urban bird populations and determine which features of the urban landscape impact mortality risk during the post‐fledging stage. From 2012–2014, we tracked 127 fledglings (60 Gray Catbirds and 67 Wood Thrushes). Over 55 days after fledging, cumulative survival of Gray Catbirds (0.32 [95% CI: 0.22–0.47]) was approximately half that of Wood Thrushes (0.63 [95% CI: 0.52–0.75]). Thus, survival rates during the post‐fledging stage, taken in isolation, do not explain differential trajectories of Gray Catbird and Wood Thrush populations in urban environments. Most mortality (86%) for both species was due to predation. However, after reaching independence from parental care, 6 birds (9.4% of mortalities) died of anthropogenic causes (e.g. building, car strikes). Crossing roads significantly increased mortality risk, but increasing daily movement distance decreased mortality risk. Our results raise the question of whether anthropogenic sources of mortality are compensatory or additive to natural mortality; we emphasize the need to monitor fledgling survival beyond the parental‐dependence stage in order to fully understand the impacts of anthropogenic hazards on juvenile birds.

opencc-zeroDec 2017View details →
dryad32/100

Data from: Lizards on newly created islands independently and rapidly adapt in morphology and diet

Rapid adaptive changes can result from the drastic alterations humans impose on ecosystems. For example, flooding large areas for hydroelectric dams converts mountaintops into islands and leaves surviving populations in a new environment. We report differences in morphology and diet of the termite-eating gecko Gymnodactylus amarali between five such newly created islands and five nearby mainland sites located in the Brazilian Cerrado, a biodiversity hotspot. Mean prey size and dietary prey-size breadth were larger on islands than mainlands, expected because four larger lizard species that also consume termites, but presumably prefer larger prey, went extinct on the islands. In addition, island populations had larger heads relative to their body length than mainland populations; larger heads are more suited to the larger prey taken, and disproportionately larger heads allow that functional advantage without an increase in energetic requirements resulting from larger body size. Parallel morphological evolution is strongly suggested, because there are indications that, before flooding, relative head size did not differ between future island and future mainland sites. Females and males showed the same trend of relatively larger heads on islands, so the difference between island and mainland sites is unlikely to be due to greater male–male competition for mates on islands. We thus discovered a very fast (at most 15 y) case of independent parallel adaptive change in response to catastrophic human disturbance.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Trunk dental tissue evolved independently from underlying dermal bony plates but is associated to surface bones in living odontode-bearing catfish

Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes. We examined the location and cover of odontodes and trunk dermal bony plates for all six loricarioid families and 17 non-loricarioid catfish families for comparison. We inferred the phylogeny of Loricarioidei using a new 10-gene dataset, eight time-calibration points, and noise-reduction techniques. Based on this phylogeny, we reconstructed the ancestral states of odontode and bony plate cover, and find that trunk odontodes emerged before dermal bony plates in Loricarioidei. Yet we discovered that when bony plates are absent, other surface bones are always associated with odontodes, suggesting a link between osteogenic and odontogenic developmental pathways, and indicating a remarkable trunk odontogenic potential in Loricarioidei.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Street lighting: sex-independent impacts on moth movement

1.Artificial lights have become an integral and welcome part of our urban and peri-urban environments. However, recent research has highlighted the potentially negative ecological consequences of ubiquitous artificial light. In particular, insects, especially moths, are expected to be negatively impacted by the presence of artificial lights. Previous research with light traps has shown a male-biased attraction to light in moths. 2.In this study, we sought to determine if street lights could limit moth dispersal and if there was any sex bias in attraction to light. More specifically, we aimed to determine sex specific attraction radii for moths to street lights. 3.We tested these hypotheses by collecting moths for two years at an experimental setup. To estimate the attraction radii we developed a Markov model and related it to the acquired data. 4.Utilizing multinomial statistics, we found that attraction rates to lights in the middle of the matrix were substantially lower than predicted by the null hypothesis of equal attraction level (0.44 times). With the Markov model, we estimated that a corner-light was 2.77 times more attractive than a wing-light with an equivalent attraction radius of c. 23m around each light. We found neither sexual differences in the attraction rate nor in the attraction radius of males and females. Since we captured three times more males than females, we conclude that sex ratios are representative of operational sex ratios or of different flight activities. 5.These results provide evidence for street lights to limit moth dispersal, and that they seem to act equally on male and female moths. Consequently, public lighting might divide a suitable landscape into many small habitats. Therefore, it is reasonable to assume i) that public lighting near hedges and bushes or field margins reduces the quality of these important habitat structures, and ii) that public lighting near important habitat structures but not interfering with local movement may affect moth movement between patches.

opencc-zeroDec 2015View details →
dryad32/100

Data from: Independent reversals to terrestriality in squirrels (Rodentia: Sciuridae) support ecologically mediated modes of adaptation

The family Sciuridae is one of the most widespread and ecologically diverse lineage of rodents and represents an ideal model for investigating the evolution of locomotion modes and the historical biogeography of terrestrial mammals. We used a comprehensive database on locomotion modes, an updated phylogeny and novel biogeographic comparative methods to re-assess the evolution of locomotion of squirrels and to investigate if these locomotion modes evolved convergently in different continents. We found that locomotion changes occurred in different independent lineages of the family, including four reversals to terrestriality and one evolution of gliding. We also found evidence for Eurasia as the center of origin of Sciuridae, challenging the classification of the oldest squirrel fossil records from the early Oligocene in North America. Additionally, Eurasia is also the possible center of origin for most of squirrel sub-families and tribes, and where locomotion changes have occurred. Parallel locomotion shifts could be explained by the adaptation towards different ecological niches followed by colonization of new continents.

opencc-zeroDec 2015View details →
dryad32/100

Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing

<p>Allopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species may lead to the origin of different taxa has received little attention. Here we used a new progenitor-specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, <i>Achillea alpina</i> and <i>A. wilsoniana</i>, via allotetraploidy from the same diploid progenitor species pair, <i>A. acuminata</i> and <i>A. asiatica</i>. Based on the sequences of 17 nuclear genes from 21 wild populations of the four <i>Achillea </i>species investigated, a clear view of  genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, <i>A. acuminata</i>, and ancestors belonging to those two groups contributed to the two tetraploid species, respectively. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study demonstrates that independent allopolyploidization events between the same <i>Achillea</i> parental species have generated two genetically and ecologically distinct taxa.</p>

opencc-zeroOct 2019View details →
dryad32/100

Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction-site-associated DNA sequencing-derived SNPs to explore fine-scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values &gt;0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.

opencc-zeroDec 2016View details →
dryad32/100

Data from: A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species of Nemertea spanning the diversity of the phylum, including representatives of 10 families and all three orders. We generated a phylogenetic framework using sequence data to reconstruct the evolutionary history of head and tail regenerative ability across the phylum and found that all evaluated species can remake a posterior end but surprisingly few could regenerate a complete head. Our analysis reconstructs a nemertean ancestor unable to regenerate a head and indicates independent gains of head regenerative ability in at least four separate lineages, with one of these gains taking place as recently as the last 10-15 mya. Our study highlights nemerteans as a valuable group for studying evolution of regeneration and identifying mechanisms associated with repeated gains of regenerative ability.

opencc-zeroDec 2018View details →
dryad32/100

Data from: Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here we ask whether convergent evolution of pad-bearing lizards have followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian Motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian Motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Wolbachia-induced meiotic drive and feminization is associated with an independent occurrence of selective mitochondrial sweep in a butterfly

Maternally inherited Wolbachia endosymbionts manipulate arthropod reproduction in various ways. In the butterfly Eurema mandarina, a cytoplasmic incompatibility-inducing Wolbachia strain wCI and the associated mtDNA haplotypes are known to originate from the sister species Eurema hecabe, which offered a good case study for microbe-mediated hybrid introgression. Besides wCI, some females with the Z0 karyotype harbour a distinct Wolbachia strain wFem, which causes all-female production by meiotic drive and feminization. We report that a considerable proportion of E. mandarina females (65.7%) were infected with both wCI and wFem (CF) on Tanegashima Island. While females singly infected with wCI (C) produced offspring at a 1 : 1 sex ratio, CF females produced only females. Although Z-linked sequence polymorphism showed no signs of divergence between C and CF females, mtDNA split into two discrete clades; one consisted of C females and the other CF females, both of which formed a clade with E. hecabe but not with uninfected E. mandarina. This suggests that CF matrilines also, but independently, experienced a selective sweep after hybrid introgression from E. hecabe. Distinct evolutionary forces were suggested to have caused C and CF matrilines to diverge, which would be irreversible because of the particular phenotype of wFem.

opencc-zeroDec 2016View details →
dryad32/100

Data from: Phylogeography of western Mediterranean Cymbalaria (Plantaginaceae) reveals two independent long-distance dispersals and entails new taxonomic circumscriptions

The Balearic Islands, Corsica and Sardinia (BCS) constitute biodiversity hotspots in the western Mediterranean Basin. Oligocene connections and long distance dispersal events have been suggested to cause presence of BCS shared endemic species. One of them is Cymbalaria aequitriloba, which, together with three additional species, constitute a polyploid clade endemic to BCS. Combining amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequences and morphometrics, we inferred the phylogeography of the group and evaluated the species' current taxonomic circumscriptions. Based on morphometric and AFLP data we propose a new circumscription for C. fragilis to additionally comprise a group of populations with intermediate morphological characters previously included in C. aequitriloba. Consequently, we suggest to change the IUCN category of C. fragilis from critically endangered (CR) to near threatened (NT). Both morphology and AFLP data support the current taxonomy of the single island endemics C. hepaticifolia and C. muelleri. The four species had a common origin in Corsica-Sardinia, and two long-distance dispersal events to the Balearic Islands were inferred. Finally, plastid DNA data suggest that interspecific gene flow took place where two species co-occur.

opencc-zeroDec 2017View details →
zenodo32/100

Differential cytotoxicity induced by the titanium(IV)salan complex Tc52in G2-phase independent of DNA damage

<p>Chemotherapy is one of the major treatment modalities for cancer. Metal-based compounds such as derivatives of cisplatin are in the front line of therapy against a subset of cancers, but their use is restricted by severe side-effects and the induction of resistance in treated tumors. Subsequent research focused on development of cytotoxic metal-complexes without cross-resistance to cisplatin and reduced side-effects. This led to the discovery of first-generation titanium(IV)salan complexes, which reached clinical trials but lacked efficacy. New-generation titanium (IV)salan-complexes show promising anti-tumor activity in mice, but their molecular mechanism of cytotoxicity is completely unknown.</p> <p>4 different human cell lines were analyzed in their responses to a toxic (Tc52) and a structurally highly related but non-toxic (Tc53) titanium(IV)salan complex. Viability assays were used to reveal a suitable treatment range, flow-cytometry analysis was performed to monitor the impact of dosage and treatment time on cell-cycle distribution and cell death. Potential DNA strand break induction and crosslinking was investigated by immunostaining of damage markers as well as automated fluorometric analysis of DNA unwinding. Changes in nuclear morphology were analyzed by DAPI staining. Acidic beta-galactosidase activity together with morphological changes was monitored to detect cellular senescence. Western blotting was used to analyze induction of pro-apoptotic markers such as activated caspase7 and cleavage of PARP1, and general stress kinase p38.</p> <p>Here we show that the titanium(IV)salan Tc52 is effective in inducing cell death in the lower micromolar range. Surprisingly, Tc52 does not target DNA contrary to expectations deduced from the reported activity of other titanium complexes. Instead, Tc52 application interferes with progression from G2-phase into mitosis and induces apoptotic cell death in tested tumor cells. Contrarily, human fibroblasts undergo senescence in a time and dose-dependent manner. As deduced from fluorescence studies, the potential cellular target seems to be the cytoskeleton.</p> <p>In summary, we could demonstrate in four different human cell lines that tumor cells were specifically killed without induction of major cytotoxicity in non-tumorigenic cells. Absence of DNA damaging activity and the cell-cycle block in G2 instead of mitosis makes Tc52 an attractive compound for further investigations in cancer treatment.</p>

opencc-zeroDec 2015View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record