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3,878 results for “Molecular Data”
Data from: Morphological and molecular evolution and their consequences for conservation and taxonomy in the Le Conte's Thrasher (Toxostoma lecontei)
We evaluated geographic variation and subspecific taxonomy in the Le Conte's Thrasher (Toxostoma lecontei) by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140,000 years ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaino Thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention.
Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances
While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may be co-extracted. Another critical step consist in carefully select suitable group-specific primer sets that should only amplify prey DNA from the targeted taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analyzed using both morphological and molecular methods. We tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate and Plant sequences and four were finally selected to be use as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp DNA stool mini kit, DNeasy mericon food kit and two CTAB-based methods) were compared using four variables: DNA concentration, A260/A280 absorbance ratio, food compartment analyzed (stomach or fecal contents), total number of prey specific PCR amplification per sample. Our results clearly indicate that the A260/A280 absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy mericon food kit (Qiagen), which yielded results very similar to those achieved with the morphological approach.
Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
Data from: Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae
A large proportion of the faunal biomass in hydrothermal vent ecosystems relies on symbiotic relationships, with bacteria as a source of nutrition. Whereas multiple symbioses have been observed in diverse vent hosts, siboglinid tubeworms have been thought to harbour a single endosymbiont phylotype affiliated to the Gammaproteobacteria. In the case of the Northeast Pacific vestimentiferan Ridgeia piscesae, two previous studies suggested the presence of more than one symbiont. The possibility of multiple, and possibly habitat-specific, symbionts in R. piscesae provided a potential explanation for the tubeworm's broad ecological niche, compared with other hydrothermal vent siboglinids. This study further explored the diversity of trophosome bacteria in R. piscesae using two methodological approaches not yet applied to this symbiosis. We carried out 454-pyrosequencing on trophosome samples from 46 individual worms and used catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) to verify the presence of the major groups detected in the pyrotag data. Both methods yielded inconsistent and sometimes contradictory results between sampling sites, and neither provided irrefutable evidence for the presence of symbionts other than the expected Gammaproteobacteria. We therefore conclude that the other adaptive mechanisms must be considered to explain the broad physico-chemical niche occupied by the different growth forms of R. piscesae.
Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck
Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from panmixia to deep, reciprocally monophyletic lineages. Yet these studies generally found weak or no nuclear (nu) DNA structure which was often attributed to sex-biased gene flow (i.e., male dispersal and female philopatry), a common behavior within this family. An alternative explanation for this "conflict" is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA leads to different signals of population structure. To test these alternatives, we simulated expected nuDNA differentiation based on mtDNA patterns of effective population sizes, gene flow, and divergence times in a Holarctic pair of waterfowl subspecies, the goosander (Mergus merganser merganser) and common merganser (M. m. americanus). We compared simulated results to empirical data from 12 nuDNA introns sampled from the species' global range. Between Europe and North America, nuDNA ФST was 3.4-fold lower than mtDNA ФST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA ФST values were generally < 0 and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by non-molecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.
Data from: A new earthworm species within a controversial genus: Eiseniona gerardoi sp. n. (Annelida, Lumbricidae) - description based on morphological and molecular data.
The morphological and anatomical simplicity of soil dwelling animals, such as earthworms, has limited the establishment of a robust taxonomy making it sometimes subjective to authors' criteria. Within this context, integrative approaches including molecular information are becoming more popular to solve the phylogenetic positioning of conflictive taxa. Here we present the description of a new lumbricid species from the region of Extremadura (Spain), Eiseniona gerardoi sp. n. The assignment to this genus is based on both a morphological and a phylogenetic study. The validity of the genus Eiseniona, one of the most controversial within Lumbricidae, is discussed. A synopsis of the differences between the type species and the west-European members of the genus is provided.
Data from: Molecular phylogeny of an ancient rodent family (Aplodontiidae)
The family Aplodontiidae contains a single, monotypic extant genus, Aplodontia (mountain beaver), which was 1st described by Rafinesque in 1817. Phylogenetic studies have shown that it is the sister lineage to squirrels. Aplodontia rufa is endemic to the Pacific Northwest and ranges from central California to British Columbia. Currently, 7 described subspecies are recognized based on morphological taxonomic studies. In this study, mitochondrial and nuclear genes were sequenced to infer molecular phylogenies of A. rufa. One of the goals of this study was to test the current taxonomic hypothesis based on morphology with molecular data. Another goal was to incorporate geographic information to elucidate distributions of major clades. Our results support the previously held subspecies designations based on morphological taxonomy, with 1 main exception: we determined that within A. rufa, the subspecies A. rufa rainieri and A. rufa rufa north of the Columbia River represent a single lineage and should revert to the name A. rufa olympica. Although we revised geographic boundaries for some groups (A. r. rufa, A. r. olympica, A. r. pacifica), only the conservation status and management of A. r. olympica (previously 2 subspecies) in Canada may be affected. Our findings support the continued conservation efforts for the isolated and endangered lineages present in coastal California.
Data from: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach
In recent years, the explosion of affordable next generation sequencing technology has provided an unprecedented opportunity to conduct genome-wide studies of adaptive evolution in organisms previously lacking extensive genomic resources. Here, we characterise genome-wide patterns of variability and differentiation using pooled DNA from eight populations of the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and pond environments. We developed a novel genome complexity reduction protocol, defined as paired-end double restriction-site associated DNA (PE dRAD), to maximise read coverage at sequenced locations. This allowed us to identify over 114,000 short consensus sequences and 15,000 SNPs throughout the genome. A total of 6,834 SNPs mapped to a single position on the related three-spined stickleback genome, allowing the detection of genomic regions affected by divergent and balancing selection, both between species and between freshwater and marine populations of the nine-spined stickleback. Gene ontology (GO) analysis revealed 15 genomic regions with elevated diversity, enriched for genes involved in functions including immunity, chemical stimulus response, lipid metabolism and signalling pathways. Comparisons of marine and freshwater populations identified nine regions with elevated differentiation related to kidney development, immunity and MAP kinase pathways. In addition, our analysis revealed that a large proportion of the identified SNPs mapping to LG XII are likely to represent alternative alleles from divergent X and Y chromosomes, rather than true autosomal markers following Mendelian segregation. Our work demonstrates how population-wide sequencing and combining inter- and intra-specific RAD analysis can uncover genome-wide patterns of differentiation and adaptations in a non-model species.
Data from: A phylogeny and evolutionary natural history of Mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data
We combine mitochondrial and nuclear DNA sequence data with non-molecular (morphological and natural history) data to conduct phylogenetic analyses and generate an evolutionary hypothesis for the relationships among nearly every species of Mesoamerican bufonid in the genus Incilius. We collected a total of 5,898 aligned base-pairs (bp) of sequence data from mitochondrial (mtDNA: 12S–16S, cyt b, ND2–CO1, including tRNAsTRP–TYR and the origin of light strand replication; total 4,317 bp) and nuclear (CXCR4 and RAG1; total 1,581 bp) loci from 52 individuals representing 37 species. For the non-molecular data, we collected 44 characters from 29 species. We also include Crepidophryne, a genus that has not previously been included in molecular analyses. We present results of parsimony and Bayesian analyses for these data separately and combined. Relationships based on the non-molecular data were poorly supported and did not resolve a monophyletic Incilius (Rhinella marina was nested within). Our molecular data provide significant support to most of the relationships. Our combined analyses demonstrate that inclusion of a considerably smaller dataset (44 vs. 5,898 characters) of non-molecular characters can provide significant support where the molecular relationships were lacking support. Our combined results indicate that Crepidophryne is nested within Incilius; therefore, we place the former in the synonymy of the latter taxon. Our study provides the most comprehensive evolutionary framework for Mesoamerican bufonids (Incilius), which we use as a starting point to invoke discussion on the evolution of their unique natural history traits.
Data from: Testing the validity of functional response models using molecular gut content analysis for prey choice in soil predators
Analysis of predator - prey interactions is a core concept of animal ecology, explaining structure and dynamics of animal food webs. Measuring the functional response, i.e. the intake rate of a consumer as a function of prey density, is a powerful method to predict the strength of trophic links and assess motives of prey choice, particularly in arthropod communities. However, due to their reductionist set-up, functional responses, which are based on laboratory feeding experiments, may not display field conditions, possibly leading to skewed results. Here, we tested the validity of functional responses of centipede predators and their prey by comparing them with empirical gut content data from field-collected predators. Our predator - prey system included lithobiid and geophilomorph centipedes, abundant and widespread predators of forest soils and their soil-dwelling prey. First, we calculated the body size-dependent functional responses of centipedes using a published functional response model in which we included natural prey abundances and animal body masses. This allowed us to calculate relative proportions of specific prey taxa in the centipede diet. In a second step, we screened field-collected centipedes for DNA of eight abundant soil-living prey taxa and estimated their body size-dependent proportion of feeding events. We subsequently compared empirical data for each of the eight prey taxa, on proportional feeding events with functional response-derived data on prey proportions expected in the gut, showing that both approaches significantly correlate in five out of eight predator - prey links for lithobiid centipedes but only in one case for geophilomorph centipedes. Our findings suggest that purely allometric functional response models, which are based on predator-prey body size ratios are too simple to explain predator - prey interactions in a complex system such as soil. We therefore stress that specific prey traits, such as defence mechanisms, must be considered for accurate predictions.
Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia
Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range-wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region.
Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
Data from: Molecular characterisation of trophic ecology within an island radiation of insect herbivores (Curculionidae: Entiminae: Cratopus).
The phytophagous beetle family Curculionidae is the most species-rich insect family known, with much of this diversity having been attributed to both co-evolution with food plants and host-shifts at key points within the early evolutionary history of the group. Less well understood is the extent to which patterns of host use vary within or among related species, largely because of the technical difficulties associated with quantifying this. Here we develop a recently characterised molecular approach to quantify diet within and between two closely related species of weevil occurring primarily within dry forests on the island of Mauritius. Our aim is to quantify dietary variation across populations and assess adaptive and non-adaptive explanations for this, and to characterise the nature of a trophic shift within an ecologically distinct population within one of the species. We find that our study species are polyphagous, consuming a much wider range of plants than would be suggested by the literature. Our data suggest that local diet variation is largely explained by food availability, and locally specialist populations consume food plants that are not phylogenetically novel, but do appear to represent a novel preference. Our results demonstrate the power of molecular methods to unambiguously quantify dietary variation across populations of insect herbivores, providing a valuable approach to understanding trophic interactions within and among local plant and insect herbivore communities.
Data from: Morphological vs. molecular delineation of taxa across montane regions in Europe: the case study of Gammarus balcanicus Schäferna, 1922 (Crustacea: Amphipoda)
Mountainous areas are characterized by substantial biodiversity and endemicity due to their complex geological history and habitat fragmentation. Hence, it can be assumed that particularly high species richness can be found in organisms with limited dispersal capabilities that inhabit mountain streams. A number of scientific papers focus on molecular phylogeography or traditional taxonomy of species or species groups inhabiting such habitats. However, there is a lack of studies that integrate morphological and molecular data to identify and delineate cryptic species. For practical reasons, uncovering cryptic diversity is crucial in taxa used in biomonitoring. Distinct species, hard to separate based on morphology only, may have different tolerance ranges towards a variety of factors. Thus, our goal is to combine the two approaches to reveal potential patterns of diversification within a species widely distributed across European mountains: the amphipod crustacean Gammarus balcanicus. The data were obtained from 13 populations spread across the range of the species. Individuals were initially ascribed to G. balcanicus based on conventional fauna key morpho-anatomical diagnostic features and were further analysed for 23 additional features to explore any putative diversification. Morphometric data were analysed with use of the multiple correspondence analysis and anova. Molecular distances were calculated for 551-bp-long COI sequences. Test for isolation by distance was performed for both morphological and molecular data. The morphometric studies showed that some of the analysed features differed significantly between populations, although there was only a weak correlation between the morphological divergence and the between-population geographical distances. Moreover, high morphological diversity was present within sites. A set of 42 COI haplotypes was identified among the 135 individuals sequenced. No haplotype was shared among populations. The molecular p-distances within the nine localities presenting more than one haplotype were either almost null (ca. <0.003 for 7 localities) or relatively low (ca. 0.01–0.02 for 2 localities). In opposite, the molecular p-distances between localities were mostly at a high level (94% of pairwise comparisons being >0.14), similar as between other well-defined species of the genus Gammarus. Surprisingly, G. balcanicus appears to be polyphyletic based on topology of the neighbour-joining tree. The level of genetic distance between localities was not correlated with their geographical proximity. Globally, combining spatial patterns of morphological versus molecular divergence indicates a high level of cryptic diversity within a species conventionally defined based upon fauna key morphological features. In this context, the name G. balcanicus should be applied only to the population from locus typicus, while the other populations represent a number of putative distinct species. We may expect that such phenomenon would apply also to other animal taxa with conserved morphology, which are widespread over different mountain ranges in Europe.
Data from: A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity
Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades.
Data from: Thelomma ocellatum, a range extension to the Yukon Territory and case study in the use of molecular data to recognize asexually reproducing crustose lichens
An unusual sterile, asexually reproducing crustose lichen was encountered during fieldwork in the Yukon Territory of Canada. Genus and family level placement of the taxon were precluded by a lack of both sexual characters and any non-sexual characters that would have suggested an unambiguous generic affiliation. Examination of mtSSU and nrITS sequence data of the taxon revealed it to be a member of the Caliciaceae, with a sister relationship to the genus Tholurna. Subsequent molecular phylogenetic analyses of mtSSU sequence data suggested conspecificity with Thelomma ocellatum, one of the few calicioid lichens that reproduce asexually via lichenized diaspores. Comparison of the material from the Yukon with reference specimens and descriptions of T. ocellatum confirmed the identification of these populations, which extend the known distribution of T. ocellatum considerably northward in North America.
Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were constructed: dataset 1, which included 12 loci totalling 9927 bp for 94 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood analyses strongly supported the monophyly of Gracillariidae and most previously recognized subfamilies and genus groups. On this basis, we propose a new classification consisting of eight subfamilies, four of which are newly recognized or resurrected: Acrocercopinae Kawahara & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae Stainton; Marmarinae Kawahara & Ohshima subfam. n.; Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is restricted to the monophyletic group comprising Gracillaria Haworth and closely related genera. We also formally transfer Acrocercops scriptulata Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating Diphtheroptila scriptulata comb. n. An exploratory mapping of larval host-use traits on the phylogeny shows strong conservation of modes of leaf mining but much higher lability of associations with host plant orders and families, suggesting that host shifts could play a significant role in gracillariid diversification.
Data from: Molecular Inversion Probes for targeted resequencing in non-model organisms
Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications
Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.
Data from: The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia
The taxonomy of the North American apodetiate and superficially apodetiate species of Cladonia with persistent, primarily squamulose thalli (viz., C. apodocarpa, C. caespiticia, and C. petrophila) is revised using morphological, chemical, and ecological data in combination with molecular phylogenetic analyses of ITS1, 5.8S, and ITS2 sequence data. The results of this approach confirm some established taxonomic concepts in the group and raise doubts about others. The taxon known as C. apodocarpa is well supported by likelihood- and parsimony-based molecular phylogenetic inferences as well as morphology, chemistry, and ecology. However, molecular evidence gives an equivocal answer to the question of whether C. petrophila is a distinct monophyletic entity or if C. apodocarpa is nested within it. In addition, no phylogenetic structure is detected for the chemical races of C. petrophila with and without fumarprotocetraric acid, based on the markers used in these analyses. However, C. petrophila does remain well supported as a taxon by chemistry (i.e., the presence of sphaerophorin), morphology, and ecology. A morphologically and ecologically distinct new taxon is described as C. stipitata. We confirm the distant relationship of these taxa (C. apodocarpa, C. petrophila, and C. stipitata) to C. caespiticia, a species with stipitate or pseudopodetiate (vs. sessile) apothecia. A treatment of the North American apodetiate species of Cladonia including distribution maps, cited specimens, and illustrations is presented. A key to the taxa that includes unrelated, frequently sterile species of Cladonia found in eastern North America is also provided.
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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.