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Data from: Multiple forms of selection shape reproductive isolation in a primate hybrid zone
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process and it has been widely assumed that reproductive isolation often results as a byproduct of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process is still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analyzing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
Data from: Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles
Behavioral isolation is thought to arise early in speciation due to differential sexual and/or natural selection favoring different preferences and traits in different lineages. Alternatively, behavioral isolation can arise due to reinforcement favoring traits and preferences that prevent maladaptive hybridization. In darters, female preference for male coloration has been hypothesized to drive speciation, because behavioral isolation evolves before F1 inviability. However, as with many long-lived organisms, the fitness of second generation hybrids has not been assessed because raising animals to adulthood in the lab is challenging. Recently, reinforcement of male preferences has been implicated in darters because male preference for conspecific females is high in sympatry but absent in allopatry in multiple species pairs. The hypothesis that reinforcement accounts for behavioral isolation in sympatry assumes that hybridization and postzygotic isolation are present. Here, we used genomic and morphological data to demonstrate that hybridization is ongoing between orangethroat and rainbow darters and used hybrids collected from nature to measure postzygotic barriers across two hybrid generations. We observed sex ratio distortion in adult F1s and a dramatic reduction in backcross survival. Our findings indicate that selection to avoid hybridization promotes the evolution of male-driven behavioral isolation via reinforcement in this system.
Data from: Strong premating reproductive isolation drives incipient speciation in Mimulus aurantiacus
Determining which forms of reproductive isolation have the biggest impact on the process of divergence is a major goal of speciation research. These barriers are often divided into those that affect the potential for hybridization (premating isolation), and those that occur after mating (postmating isolation), and much debate has surrounded the relative importance of these categories. Within the species Mimulus aurantiacus, red- and yellow-flowered ecotypes occur in the southwest corner of California, and a hybrid zone occurs where their ranges overlap. We show that premating barriers are exclusively responsible for isolation in this system, with both ecogeographic and pollinator isolation contributing significantly to total isolation. Postmating forms of reproductive isolation have little or no impact on gene flow, indicating that hybrids likely contribute to introgression at neutral loci. Analysis of molecular variation across thousands of RAD-seq markers reveals that the genomes of these taxa are largely undifferentiated. However, structure analysis shows that these taxa are distinguishable genetically, likely due to the impact of loci underlying differentiated adaptive phenotypes. These data exhibit the power of divergent natural selection to maintain highly differentiated phenotypes in the face of gene flow during the early stages of speciation.
Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species
PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.
Data from: Isolation of Metrosideros (`Ohi`a) taxa on O`ahu increases with elevation and extreme environments
<p>Species radiations should be facilitated by short generation times and limited dispersal among discontinuous populations. Hawaii's hyper-diverse, landscape-dominant tree,<br> <em>Metrosideros</em>, is unique among the islands' radiations for its massive populations that occur continuously over space and time within islands, its exceptional capacity for gene flow by both pollen and seed, and its extended life span (ca. >650 years). <em>Metrosideros</em> shows the greatest phenotypic and microsatellite DNA diversity on O`ahu, where taxa occur in tight sympatry or parapatry in mesic and montane wet forest on two volcanoes. We document the nonrandom distributions of 12 taxa (including unnamed morphotypes) along elevation gradients, measure phenotypes of ~6-year-old common-garden plants of eight taxa to verify heritability of phenotypes, and examine genotypes of 476 wild adults at nine microsatellite loci to compare the strengths of isolation across taxa, volcanoes and distance. All eight taxa retained their diagnostic phenotypes in the common garden. Populations were isolated by taxon to a range of degrees (pairwise F<sub>ST</sub> between taxa: 0.004 – 0.267), and there was no pattern of isolation by distance or by elevation; however, significant isolation between volcanoes was observed within monotypic species, suggesting limited gene flow between volcanoes. Among the infraspecific taxa of <em>M. polymorpha</em>, genetic diversity and isolation significantly decreased and increased, respectively, with elevation. Overall, five of the six most isolated taxa were associated with highest elevations or otherwise extreme environments. These findings suggest a principal role for selection in the origin and maintenance of the exceptional diversity that occurs within continuous <em>Metrosideros</em> stands on O`ahu.</p>
The evolution of reproductive isolation in Daphnia
Background <p>The process by which populations evolve to become new species involves the emergence of various reproductive isolating barriers (RIB). Despite major advancements in understanding this complex process, very little is known about the order in which RIBs evolve or their relative contribution to the total restriction of gene flow during various stages of speciation. This is mainly due to the difficulties of studying reproductive isolation during the early stages of species formation. This study examines ecological and non-ecological RIB within and between <i>Daphnia pulex</i> and <i>Daphnia pulicaria,</i> two recently diverged species that inhabit distinct habitats and exhibit an unusual level of intraspecific genetic subdivision.</p> Results <p>We find that while ecological prezygotic barriers are close to completion, none of the non-ecological barriers can restrict gene flow between <i>D. pulex</i> and <i>D. pulicaria</i> completely when acting alone. Surprisingly, we also identified high levels of postzygotic reproductive isolation in 'conspecific' interpopulation crosses of <i>D. pulex</i>.</p> Conclusions <p>While the ecological prezygotic barriers are prevalent during the mature stages of speciation, non-ecological barriers likely dominated the early stages of speciation. This finding indicates the importance of studying the very early stages of speciation and suggests the contribution of postzygotic isolation in initiating the process of speciation.</p>
Data from: Mating patterns and post-mating isolation in three cryptic species of the Engystomops petersi species complex
Determining the extent of reproductive isolation in cryptic species with dynamic geographic ranges can give us important insights into the processes that generate and maintain genetic divergence in the absence of severe geographic barriers. We studied mating patterns, propensity to crossbreed in nature and subsequent fertilization rates, as well as survival and development of hybrid F1 offspring for three species of the E. petersi species complex in Yasuní National Park, Ecuador. We found at least two species in five out of seven locations sampled, and 14.3% of the wild pairs genotyped were heterospecific crosses. We also found reduced fertilization rates in hybrid crosses between E. petersi females and E. "magnus" males, and between E. "magnus" females and E. "selva" males but not in the opposite hybrid crosses, suggesting asymmetric reproductive isolation for these species. Larval development time decreased in F1 hybrid crosses compared to conspecific F1s, but we did not find any reduction in larval survival or early metamorph survival. Our results show evidence of post-mating isolation for at least two hybrid crosses of the cryptic species we studied. The general decrease in fertilization rates in heterospecific crosses suggests that sexual selection and reinforcement might have not only contributed to the pattern of call variation and behavioral isolation we see between species today, but they may also contribute to further signal divergence and behavioral evolution, especially in locations where hybridization is common and fertilization success is diminished.
Data from: Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of Mimulus aurantiacus
Many forms of reproductive isolation contribute to speciation, and early acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of inter‐taxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions. In Mimulus aurantiacus, red‐ and yellow‐flowered ecotypes are incompletely isolated by divergent selection exerted by different pollinators. However, these emerging taxa are largely isolated spatially, with a hybrid zone occurring along a narrow region of contact. In order to assess whether responses to abiotic conditions contribute to the parapatric distribution of ecotypes, we measured a series of ecophysiological traits from populations along a transect, including drought sensitivity, leaf area, and the concentrations of vegetative flavonoids. In contrast to the abrupt transitions in floral phenotypes, we found that ecophysiological traits exhibited a continuous geographic transition that largely mirrors variation in climatological variables. These traits may impede gene flow across a continuous environmental gradient, but they would be unlikely to result in ecotypic divergence alone. Nevertheless, we found a genetic correlation between vegetative and floral traits, providing a potential link between the two forms of isolation. Although neither barrier appears sufficient to cause divergence on its own, the combined impacts of local adaptation to abiotic conditions and regional adaptation to pollinators may interact to drive discontinuous variation in the face of gene flow in this system.
Data from: Distributional shifts – not geographic isolation – as a probable driver of montane species divergence
As biodiversity hotspots, montane regions have been a focus of research to understand the divergence process. Like their oceanic counterparts, the diversity of the "sky islands" might be ascribed to geographic isolation of mountaintops. However, because the sky islands, and especially those in northern latitudes, are subject to extreme climatic events such as the glacial cycles that drove both altitudinal and geographical shifts in species' distributions, the dynamic colonization process is also a possible factor driving divergence. Here we test these two hypotheses (i.e., isolation versus colonization) in a flightless montane grasshopper, Melanoplus oregonensis, which is a member of a diverse group that radiated across the Rocky Mountains of North America. Using approximate Bayesian computation (ABC) and spatially explicit simulations that account for spatial heterogeneity and temporal shifts in species distributions, we show that a colonization model of the sky islands from refugial populations provides a significantly better fit to the empirical genetic data than a model of the geographic isolation among sky islands. Moreover, support for the colonization model holds irrespective of whether the movement of individuals was modeled as a diffusion process or was informed by differences in habitat suitabilities across the landscape. With validation analyses to confirm the models provide a good fit to the data, as well as general power and quality analyses, the research not only adds to a growing body of work on the complex dynamics underlying montane biodiversity, but it also provides much needed evaluation of competing hypotheses based on explicit models of the divergence process, as opposed to inferences about diversification drivers from species diversity patterns.
Data from: Female mate choice is a reproductive isolating barrier in Heliconius butterflies
In sexually reproducing organisms, speciation involves the evolution of reproductive isolating mechanisms that decrease gene flow. Premating reproductive isolation, often the result of mate choice, is a major obstacle to gene flow between species because it acts earlier in the life cycle than other isolating barriers. While female choice is often considered the default mode in animal species, research in the butterfly genus Heliconius, a frequent subject of speciation studies, has focused on male mate choice. We studied mate choice by H. cydno females by pairing them with either conspecific males or males of the closely related species H. pachinus. Significantly more intraspecific trials than interspecific trials resulted in mating. Because male courtship rates did not differ between the species when we excluded males that never courted, we attribute this difference to female choice. Females also performed more acceptance behaviours towards conspecific males. Premating isolation between these two species thus entails both male and female mate choice, and female choice may be an important factor in the origin of Heliconius species.
Data from: Reproductive isolation and the maintenance of species boundaries 1 in two serpentine endemic Jewelflowers
Speciation occurs when reproductive barriers substantially reduce gene flow between lineages. Understanding how specific barriers contribute to reproductive isolation offers insight into the initial forces driving divergence, and the evolutionary and ecological processes responsible for maintaining diversity. Here we quantified multiple pre- and post-pollination isolating barriers in a pair of closely related California Jewelflowers (Streptanthus, Brassicaceae) living in an area of sympatry. S. breweri and S. hesperidis are restricted to similar serpentine habitats, however populations are spatially isolated at fine-scales and rarely co-occur in intermixed stands. Several intrinsic postzygotic barriers were among the strongest we quantified, however postzygotic barriers currently contribute little to overall reproductive isolation due to the cumulative strength of earlier-acting extrinsic barriers, including spatial isolation, and flowering time and pollinator differences. Data from multiple years suggest that pre-pollination barriers may have different strengths depending on annual environmental conditions. Similarly, crossing data suggest that the strength of intrinsic isolation may vary between different population pairs. Estimates of total reproductive isolation in S. breweri - S. hesperidis are robust to uncertainty and variability in individual barrier strength estimates, demonstrating how multiple barriers can act redundantly to prevent gene flow between close relatives living in sympatry.
Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioral and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the emerald-eyed treefrog, <i>Boana platanera</i>, distributed across an environmental gradient in Central Colombia (northern South America). We analyzed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, <i>B. platanera </i>exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Gene flow and isolation in the arid Nearctic revealed by genomic analyses of desert spiny lizards
<p>The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide, and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (<em>Sceloporus magister</em>) and Baja Spiny Lizards (<em>S. zosteromus</em>), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the <em>S. magister</em> complex is geographically structured, but we also detect instances of gene flow. The Continental Divide is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in <em>S. zosteromus</em>. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.</p>
Water supply improvement and isolation of native microalgae study at Primar Hatchery
<p>Revise the estuarine water collection and treatment structure to improve the water quality of the Primar hatchery of <i>Crassostrea gasar </i>and produce isolated native microalgae feed for larvae of <i>C. gasar</i></p><p> </p><p>Based on previous projects and literature, a system to improve the catchment structure and treatment of estuarine water used at Primar's hatchery was developed. Further, samples of native microalgae were collected at a location close to the Primar hatchery. The microalgae were isolated and experimental production, subsequent tests, evaluations and adjustments were performed before pilot production of native microalgae for feeding of <i>C. gasar</i> was done. </p><p>The data was collected during 2020 and 2023 at Primar hatchery, Brazil. </p>
Biomarkers of neurodegeneration in isolated and antidepressant-related REM sleep behavior disorder.
<p>Dataset relative to the manuscript "Biomarkers of neurodegeneration in isolated and antidepressant-related REM sleep behavior disorder."</p>
Multiple sequence alignments: Detection and isolation of a new member of Burkholderiaceae‑related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales
<p><strong>Methods:</strong></p><p>Nucleotide sequences were aligned independently for each region using MAFFT v7.212 (Katoh and Standley, 2013). The obtained alignment blocks were subject to Gblocks 0.91b (Castresana, 2000) to remove poorly aligned positions with the relaxed selection setting described in Talavera & Castresana (2007) using the following parameters (-t = d -b2 = 9 -b3 = 10 -b4 = 5 -b5 = h). After automatically removing gaps, the alignment blocks were viewed using MEGA 6.06 software (Tamura et al., 2013) and poorly aligned positions at either end of the alignments were removed manually. Pairwise distances of the nucleotide sequences (ITS2, ITS1-5.8S-ITS2, LSU, and tef1) of the ex-type strains of seven <i>Saksenaea</i> spp. and the representative isolate <i>S. boninensis</i> Sak4 were calculated by MEGA 6.06 software (Tamura et al. 2013). Multiple sequence alignment of 16S rRNA gene of the family <i>Burkholderiaceae</i> was prepared for the phylogeny of a bacterial endosymbiont. Multiple sequence alignments of ITS, LSU, and tef1 genes of <i>Saksenaea</i> spp. (Mucorales) were separately prepared for the phylogeny of a fungal host. Concatenated dataset of these genes were also prepared. All nucleotide sequences were retrieved from GenBank (See "Sequence_ID.csv" and taxon names of each alignment). </p><p> </p><p><strong>Description of files:</strong></p><p><strong>A. Phylogeny of the family </strong><i><strong>Burkholderiaceae</strong></i><strong> (Bacterial endosymbiont):</strong></p><p>1. Burkholderiaceae_16S_RAW.fasta</p><p>Non-aligned dataset of 16S rRNA gene of the family <i>Burkholderiaceae</i>.</p><p> </p><p>2. Burkholderiaceae_16S_aligned.fasta</p><p>Aligned dataset of 16S rRNA gene of the family <i>Burkholderiaceae</i>.</p><p> </p><p><strong>B. Phylogenies of </strong><i><strong>Saksenaea</strong></i><strong> spp. (Fungal host):</strong></p><p>1. Sequence_ID_v2.csv</p><p>Taxon names, accession numbers, and sequence ID for the concatenated multiple sequence alignment are listed.</p><p> </p><p>2. Saksenaea_ITS_RAW_v2.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. </p><p> </p><p>3. Saksenaea_ITS_aligned_v2.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. Only used for ITS1-5.8S-ITS2 phylogeny.</p><p> </p><p>4. Saksenaea_LSU_RAW_v2.fasta</p><p>Non-aligned dataset of LSU gene region of <i>Saksenaea</i> spp. </p><p> </p><p>5. Saksenaea_LSU_aligned_v2.fasta</p><p>Aligned dataset of LSU gene region of <i>Saksenaea</i> spp. Only used for LSU phylogeny.</p><p> </p><p>6. Saksenaea_tef1_RAW_v2.fasta</p><p>Non-aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. </p><p> </p><p>7. Saksenaea_tef1_aligned_v2.fasta</p><p>Aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. Only used for tef1 phylogeny.</p><p> </p><p><strong><Concatenated dataset 1 (ITS2, LSU, tef1)></strong></p><p>8. Saksenaea_ITS2_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 1.</p><p> </p><p>9. Saksenaea_ITS2_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 1.</p><p> </p><p>10. Saksenaea_LSU_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of LSU gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>11. Saksenaea_LSU_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of LSU gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>12. Saksenaea_tef1_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>13. Saksenaea_tef1_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of tef1 gene region of <i>Saksenaea</i> spp. used for preparation of concatenated datasets 1 and 2.</p><p> </p><p>14. Saksenaea_ITS2_LSU_tef1_concatenated_dataset1.fasta</p><p>Concatenated dataset of three multiple sequence alignments (9, 11, and 13). This concatenated dataset was used for the main phylogeny of <i>Saksenaea</i> spp.</p><p> </p><p><strong><Concatenated dataset 2 (ITS1-5.8S-ITS2, LSU, tef1)></strong></p><p>15. Saksenaea_ITS_for_concatenated_RAW_v2.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 2.</p><p> </p><p>16. Saksenaea_ITS_for_concatenated_aligned_v2.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of <i>Saksenaea</i> spp. used for preparation of a concatenated dataset 2.</p><p>Blank sequences were inserted for five isolates of <i>Saksenaea longicolla</i> after the alignment.</p><p> </p><p>17.Saksenaea_ITS_LSU_tef1_concatenated_dataset2.fasta</p><p>Concatenated dataset of three multiple sequence alignments (15, 11, and 13). This concatenated dataset was used for the main phylogeny of <i>Saksenaea</i> spp.</p><p> </p><p><strong>C. Pairwise distances of the ex-type strains of </strong><i><strong>Saksenaea</strong></i><strong> spp.</strong></p><p>1. Saksenaea_ITS_type_RAW.fasta</p><p>Non-aligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>2. Saksenaea_ITS2_type_aligned.fasta</p><p>Aligned dataset of ITS2 region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>3.Saksenaea_ITS_type_aligned.fasta</p><p>Aligned dataset of ITS1-5.8S-ITS2 region of the ex-type strains of <i>Saksenaea</i> spp. without <i>Saksenaea longicolla</i>.</p><p> </p><p>4. Saksenaea_LSU_type_RAW.fasta</p><p>Non-aligned dataset of LSU gene region of the ex-type strains of <i>Saksenaea </i>spp.</p><p> </p><p>5. Saksenaea_LSU_type_aligned.fasta</p><p>Aligned dataset of LSU gene region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>6. Saksenaea_tef1_type_RAW.fasta</p><p>Non-aligned dataset of tef1 gene region of the ex-type strains of <i>Saksenaea</i> spp.</p><p> </p><p>7. Saksenaea_tef1_type_aligned.fasta</p><p>Aligned dataset of tef1 gene region of the ex-type strains of <i>Saksenaea</i> spp.</p>
Fig. 1 in Transmission of cineraria isolate of tomato yellow ring virus by Frankliniella occidentalis and Thrips tabaci (Thysanoptera, Thripidae)
Fig. 1: Rate of transmission of TYRV-CI to petunia plants by T. tabaci and F. occidentalis.
Data for: Effects of reproductive status on behavioral and neural responses to isolated pup stimuli in female California mice
<p>The transition to motherhood in mammals is marked by changes in females' perception of and responsiveness to sensory stimuli from infants. Our understanding of maternally induced sensory plasticity relies most heavily on studies in uniparental, promiscuous house mice and rats, which may not be representative of rodent species with different life histories. We exposed biparental, monogamous California mouse (<em>Peromyscus californicus)</em> mothers and ovariectomized virgin females to one of four acoustic and olfactory stimulus combinations (Control: clean cotton and white noise; Call: clean cotton and pup vocalizations; Odor: pup-scented cotton and white noise; Call + Odor: pup-scented cotton and pup vocalizations) and quantified females' behavior and Fos expression in select brain regions. Behavior did not differ between mothers and ovariectomized virgins. Among mothers, however, those exposed to the Control condition took the longest to sniff the odor stimulus, and mothers exposed to the Odor condition were quicker to sniff the odor ball compared to those in the Call condition. Behavior did not differ among ovariectomized virgins exposed to the different conditions. Fos expression differed across conditions only in the anterior hypothalamic nucleus (AHN), which response to aversive stimuli: among mothers, the Control condition elicited the highest AHN Fos and Call + Odor elicited the lowest. Among ovariectomized virgin females, Call elicited the lowest Fos in the AHN. Thus, reproductive status in California mice alters females' behavioral responses to stimuli from pups, especially odors, and results in the inhibition of defense circuitry in response to pup stimuli.</p>
Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)
<p>Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.</p>
Characterization of a novel marine isolate Micromonospora spp BRA006 through a metabologenomics approach
<p>This repository contains the Supplementary Tables (1-3) as well as the datasets with the preprocessed data that led to the metabolomic results presented in the paper. In addition, links to the jobs using GNPS2 for the <a href="https://gnps2.org/status?task=e73b27dd85a24cee84c776739f5b05f0">FBMN</a>, <a href="https://gnps2.org/status?task=fed145fd210b48ec94cc2aae9f8f93fa">ChemWalker</a> analysis, and <a href="https://metabolomics-usi.gnps2.org/dashinterface/?usi1=mzspec%3AGNPS2%3ATASK-e73b27dd85a24cee84c776739f5b05f0-nf_output%2Fclustering%2Fspectra_reformatted.mgf%3Ascan%3A445&usi2=mzspec%3AGNPS%3AGNPS-LIBRARY%3Aaccession%3ACCMSLIB00000848810&width=10.0&height=6.0&mz_min=None&mz_max=None&max_intensity=125&annotate_precision=4&annotation_rotation=90&cosine=standard&fragment_mz_tolerance=0.1&grid=True&annotate_peaks=%5B%5B130.0653076171875%5D%2C%20%5B130.06472778320312%5D%5D">spectral pairing of Brevianamide F</a> are included.</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.