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1,918 results for “molecular evidence”
FIGURE 5 in Emesis planeca n. comb. (Lepidoptera: Riodinidae): a new combination revealed by molecular evidence with a description of its morphological variation
FIGURE 5. Male genitalia of Emesis planeca n. comb. (MZFC LEP 429988). Arrows in lateral view point at: two types of cornuti and; dorsal process of the valvae with many setae. In ventral view this process looks squared, wide and projected outwards.
FIGURE 3 in Morphological and molecular evidence of a new species of Melanochlamys (Gastropoda: Heterobranchia) from the Bohai Sea, China
FIGURE 3. Phylogenetic tree inferred by Bayesian analysis (BI) and maximum likelihood (ML) based on concatenated dataset of COI, 16S and H3 genes. Numbers adjacent to nodes refer to BI posterior probability (PP> 0.5) and ML bootstrap scores (BS> 50)
FIGURE 1 in Morphological and molecular evidence of a new species of Melanochlamys (Gastropoda: Heterobranchia) from the Bohai Sea, China
FIGURE 1. Map of sampling site of Melanochlamys aquilina sp. nov. in the Bohai Sea, 37°36′N 118°57′E, red triangle.
FIGURE 2 in Morphological and molecular evidence of a new species of Melanochlamys (Gastropoda: Heterobranchia) from the Bohai Sea, China
FIGURE 2. Melanochlamys aquilina sp. nov. A. Holotype, MBM285089, live animal, 13.5 mm in length; B, C. ventral and apical view of fragment of shell of paratype #1; D, E. Male reproductive anatomy of paratype #1 and paratype #2, respectively. Abbreviations: ex, excurrent sperm groove; m, retractor muscle; pe, penis; pr, prostate; ps, penial spine; spb, spermatic bulb.
Data from: Morphological, cellular and molecular evidences of chromosome random elimination in vivo upon haploid induction in maize
The mechanism of maternal in vivo haploid induction is not fully understood. In this study, the young embryos were identified by morphology, cytology and simple sequence repeat (SSR) markers at different developmental stages in the cross HZ514 (sweet corn) × HZI1 (inducer). The results indicated that the low seed setting rate was determined by the inducer pollen during the process of fertilization. The mosaic endosperm kernels and the different percentages of aneuploidy, mixploidy, lagged chromosome, micronuclei, chromosomal bridge and ring chromosome were found in the cross; 7.37% of the haploid embryos carried chromosome segments from HZI1. About 1% twin seedlings resulted from the cross and were analyzed by cytology and SSR markers. Four pairs of twin seedlings had different chromosome numbers (2n = 20 and 2n = 10–20) and there were some chromosome fragments from HZI1. Aneuploidy, mixploidy and the abnormal chromosomes occurred in the in vivo haploid induction by HZI1, which is the cytological basis for haploid induction and indicates that the inducer's chromosomes are prone to be lost during mitotic and meiotic divisions. Morphological, cellular and molecular evidences reveal that complete or partial chromosome elimination from inducer HZI1 controls the maize in vivo haploid induction.
Data from: Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?
Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as hybrids. Amplified fragment length polymorphism (AFLP) marker analysis was performed on 378 specimens collected from northern California and Nevada. Population structure was inferred using a Bayesian/Markov chain Monte Carlo method, which probabilistically assigns individuals to genetic clusters. Three genetic clusters provided the best fit for the data. C. eurytheme individuals were primarily assigned to two closely related clusters, and C. eriphyle individuals were mostly assigned to a third, more distantly related cluster. There appeared to be significant hybridization between the two species. Individuals of intermediate phenotype (putative hybrids) were found to be genetically indistinguishable from C. eriphyle, indicating that previous work based on the assumption that these intermediate forms are hybrids may warrant reconsideration.
Data from: Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan
Marine aquaculture and stock enhancement are major causes of the introduction of alien species. A good example of such an introduction is the Japanese shortneck clam Ruditapes philippinarum, one of the most important fishery resources in the world. To meet the domestic shortage of R. philippinarum caused by depleted catches, clams were imported to Japan from China and the Korean peninsula. The imported clam is an alien species that has a very similar morphology, and was misidentified as R. philippinarum (hereafter, Ruditapes form). We genotyped 1,186 clams of R. philippinarum and R. form at four microsatellite loci, sequenced mitochondrial DNA (COI gene fragment) of 485 clams, 34 of which were R. variegatus, and measured morphometric and meristic characters of 754 clams from 12 populations in Japan and China, including the Ariake Sea and Tokyo Bay, where large numbers of R. form were released. Our analyses confirmed that R. form was from the genus Ruditapes, and the genetic differentiation between R. philippinarum and R. form was distinct, but small, compared with five bivalve outgroups. However, R. form had distinct shell morphology, especially larger numbers of radial ribs on the shell surface, suggesting that R. form might be a new Ruditapes species or a variation of R. philippinarum that originated from southern China. A genetic affinity of the sample from the Ariake Sea to R. form was found with the intermediate shell morphology and number of radial ribs, and the hybrid proportion was estimated at 51.3 ± 4.6 % in the Ariake Sea.
Data from: Diversity of ridged frogs (Anura: Ptychadenidae: Ptychadena spp.) in wetlands of the upper Nile in Rwanda: morphological, bioacoustic, and molecular evidence
We investigated the distribution of species of the genus Ptychadena at nine sites at the upper Nile and its catchment in Rwanda. For species delimitation, we chose an integrative approach, combining morphological and bioacoustic data and DNA barcoding (mitochondrial 16S rRNA gene). We identified three species using independent evidence from the three different data sets: Ptychadena anchietae, Ptychadena porosissima, and a species of the Ptychadena mascareniensis group. The latter is undistinguishable genetically, bioacoustically, and morphologically from populations from Uganda, Kenya, and Egypt. We resurrect the name Ptychadena nilotica for these populations. The species differs strongly genetically from topotypic P. mascareniensis, and from clades referred to as P. cf. mascareniensis from Western and Central Africa. Morphologically, the three Rwandan species can be differentiated by their quantitative morphometrics (discriminant analysis, success rate: 98.3%) and by a number of qualitative characters of external morphology which are useful for identification in the field. The specific features of the advertisement call differ unequivocally among the three species and allow detection and identification in the field. We also provide quantitative descriptions of temporal and frequency structure of the release calls of two of the species and the distress calls of all three species. Finally, we compare the 16S sequences obtained from Rwandan specimens with those deposited in GenBank to estimate geographical distribution of taxa in Africa.
Data from: On merging Acer sections Rubra and Hyptiocarpa: molecular and morphological evidence
In this study, we expanded Acer sect. Rubra Pax to include A. sect. Hyptiocarpa Fang. Traditionally, section Rubra comprises two iconic species, Acer rubrum Linnaeus (red maple) and A. saccharinum Linnaeus (silver maple), of eastern North American forests as well as the rare Japanese montane species, A. pycnanthum K. Koch. Section Hyptiocarpa consists of A. laurinum Hasskarl and A. pinnatinervium Merrill, which occur in subtropical and tropical regions of southwestern China to southeast Asia. Here, we confirm prior phylogenetic results showing the close relationship between sects. Rubra and Hyptiocarpa, and we use scanning electron microscopy to demonstrate that leaves of species within these sections have similar arrangements of cuticular waxes, which account for the silvery color of their abaxial surfaces. We describe that the sections also share labile sex expression; inflorescences that range from compound racemose thyrses, to racemes or umbels and that may have undergone evolutionary reduction; and several features of their fruits, such as seed locules without keels, basal portion of wings straight, acute attachment angle between mericarps, and production of some mericarps that are seedless and partially developed at maturity. Our expansion of sect. Rubra to include sect. Hyptiocarpa better elucidates the biogeographic and evolutionary history of these species. Additionally, we show that A. laurinum and A. pinnatinervium have intergrading morphology and are probably synonymous, but we note that further studies are required to conclude their taxonomic status.
Data from: Molecular phylogenetic evidence corroborates morphology but not chemistry in the Lepraria neglecta group
The Lepraria neglecta group is a distinctive entity within the sterile, asexually reproducing lichen genus Lepraria whose constituent populations are united by their occurrence in exposed habitats and the development of a pseudocortex on the granules of the thallus. Previous studies have concluded that the group represents a monophyletic entity; however the question of how to classify the chemical variability exhibited within the group has remained unresolved. A phylogeny was inferred from ITS1, 5.8S, and ITS2 sequence data generated from a geographically and chemically broad sampling of populations within the L. neglecta group. While the inferred phylogeny recovered the core L. neglecta group as a strongly supported and monophyletic, the chemotypes within L. neglecta s.l. (i.e., the core-neglecta group excluding L. granulata) were not recovered as monophyletic and relationships within the group largely remain poorly resolved. Based on these results, a pragmatic circumscription for the group is proposed that emphasizes the strong correlation between morphological, ecological, and molecular characters over the lack of resolution between chemical and molecular characters. The names applied to members of the group are placed in synonymy with L. neglecta (these are L. alpina (basionym Crocynia alpina), L. alpina var. zeorinica, L. angardiana, L. borealis, L. caerulescens, L. caesioalba (basionym Crocynia caesioalba), L. caesioalba var. groenlandica, L. gelida, L. svalbardensis, and L. zonata). The results of these molecular phylogenetic analyses also 1) did not support the distinction of L. salazinica from L. elobata, thus that name is placed in synonymy here, and 2) elucidated the occurrence of L. humida in North America.
Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada
<p>Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (<i>sed</i>aDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (brGDGTs) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The<i> sed</i>aDNA record tightly constrains the colonization of dwarf birch (<i>Betula</i>, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic <sup>10</sup>Be moraine dating and >2 ka later than <i>Betula</i> pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding <i>Betula</i> establishment. Together, these molecular proxies reveal that <i>Betula</i> colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like <i>Betula</i>, can be compromised by both exotic pollen fluxes and vegetation migration lags.</p>
Data from: Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65–57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.
Data from: Systematics of the blindsnakes (Serpentes: Scolecophidia: Typhlopoidea) based on molecular and morphological evidence
The blindsnake superfamily Typhlopoidea (Gerrhopilidae, Typhlopidae, and Xenotyphlopidae) is a diverse, widespread part of the global snake fauna. A recent systematic revision based on molecular phylogenetic analyses and some morphological evidence presented a preliminary solution to the non-monophyly of many previously recognized genera, but additional clarification is needed regarding the recognition of some species and genera. We rectify these problems here with a new molecular phylogenetic analysis including 95 of the 275 currently recognized, extant typhlopoids, incorporating both nuclear and mitochondrial loci. We supplement this with data on the external, visceral, and hemipenial morphology of nearly all species to generate a revised classification for Typhlopoidea. Based on morphological data, we re-assign Cathetorhinus from Typhlopidae to Gerrhopilidae. Xenotyphlopidae maintains its current contents (Xenotyphlops). In Typhlopidae, one monotypic genus is synonymized with its larger sister-group as it cannot be unambiguously diagnosed morphologically (Sundatyphlops with Anilios), and two genera are synonymized with Typhlops (Antillotyphlops and Cubatyphlops), as they are not reciprocally monophyletic. The genus Asiatyphylops is renamed Argyrophis, the senior synonym for the group. We erect one new genus (Lemuriatyphlops) for a phylogenetically distinct species-group in Asiatyphlopinae. Fourteen of eighteen recognized typhlopid genera are maintained in four subfamilies: Afrotyphlopinae (Afrotyphlops, Grypotyphlops [re-assigned from Asiatyphlopinae], Letheobia, and Rhinotyphlops), Asiatyphlopinae (Acutotyphlops, Anilios, Cyclotyphlops, Indotyphlops, Malayotyphlops, Ramphotyphlops, and Xerotyphlops), Madatyphlopinae (Madatyphlops), and Typhlopinae (Amerotyphlops and Typhlops), some with altered contents. Diagnoses based on morphology are provided for all 19 typhlopoid genera, accounting for all 275 species. This taxonomy provides a robust platform for future revisions and description of new species.
FIGURE 5 in The limits of polymorphism in Liolaemus rothi: Molecular and phenotypic evidence for a new species of the Liolaemus boulengeri clade (Iguanidae, Liolaemini) from boreal Patagonia of Chile
FIGURE 5. Map of the North-Western Patagonia of Argentina and Chile, showing the distribution of Liolaemus hermannunezi (black circle), L. rothi (empty circles), L. sagei (cross), and L. loboi (black triangle). Details on the wide Patagonian geographical distribution of L. rothi can be found in Cei (1986)
FIGURE 4 in The limits of polymorphism in Liolaemus rothi: Molecular and phenotypic evidence for a new species of the Liolaemus boulengeri clade (Iguanidae, Liolaemini) from boreal Patagonia of Chile
FIGURE 4. Holotype of Liolaemus hermannunezi, male, MNHNC 3785, from 10 km E of Los Barros, near Pichachén Pass, Eighth Region, Chile. Photo D. Pincheira-Donoso.
FIGURE 3. Phylogenetic relationships among 67 in The limits of polymorphism in Liolaemus rothi: Molecular and phenotypic evidence for a new species of the Liolaemus boulengeri clade (Iguanidae, Liolaemini) from boreal Patagonia of Chile
FIGURE 3. Phylogenetic relationships among 67 Liolaemini taxa based on maximum parsimony analysis of 1710 aligned positions of DNA sequence data (length = 5810 steps). Strict consensus of five equally most parsimonious trees. Bootstrap values are presented above branches and decay indices are shown in bold below branches on the cladogram.
FIGURE 2 in The limits of polymorphism in Liolaemus rothi: Molecular and phenotypic evidence for a new species of the Liolaemus boulengeri clade (Iguanidae, Liolaemini) from boreal Patagonia of Chile
FIGURE 2. (a) Adult male of L. hermannunezi in life. Specimen collected approximately 8 km E of Los Barros, Laguna del Laja, Chile; (b) adult female from the same locality. Photos J. A. Schulte.
FIGURE 3 in Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding
FIGURE 3. Geographic distribution of Dipturus argentinensis n. sp. based on material collected. Symbols represent more than one capture. Star indicates original locality of holotype.
FIGURE 2 in Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding
FIGURE 2. Tail thorns of Dipturus argentinensis n. sp., immature male paratype (INIDEP 797, 617 mm TL) (A), Dipturus chilensis, immature female (INIDEP 547, 715 mm TL) (B), and Dipturus trachyderma, immature male (INIDEP 789, 1211 mm TL) (C).
FIGURE 1. Dipturus argentinensis n in Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding
FIGURE 1. Dipturus argentinensis n. sp., holotype, INIDEP 793, 765 mm TL, juvenile male, off central Patagonian shelf, Argentina. a–dorsal view; b– ventral view.
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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.