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539 results for “disentangling”
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a number of new lineages (L1–L13) identified in our study. The lineages are marked with grey bars which represent the criteria used to delimit species boundaries, where three gene bPTP (P3), genetic p-distance (GD), morphological separation (M) and geographic isolation (G) are used to predict the number of putative lineages. The nodes below 70% parametric bootstrap support are indicated with asterisk (*). "+" indicates that the status of A. nasuta cf. isabellina needs further work (see Deepak et al. 2019).
FIGURE 16 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 16. Habitat of Ahaetulla malabarica sp. nov. in Brahmagiri Hills, Central Western Ghats (borders Kodagu district, Karnataka State and Waynad district, Kerala State, India) showing semi-evergreen and evergreen forest vegetation types.
FIGURE 9 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 9. Reproductions of colour plates of (a) Coluber nasutus (La Nasique) from Lacepede (1789: 302, pl. 4); (b) Dryinus oxyrhynchus (Passeriki Pam) from Russell (1796: pl. 12); (c) Dryinus russellianus (Botla Passeriki) from Russell (1796: pl. 13); (d) Photo of the preserved skin of BMNH 1904.7.27.25 Dryophis passeriki Photo: Gernot Vogel.
FIGURE 8 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 8. Images of live uncollected Ahaetulla nasuta from Kandy, Sri Lanka (a) Head dorsal, (b) Head lateral, (c) body lateral, (d) body ventrolateral, (e) entire dorsal, (f) [inset] ventral view of specimen with brownish venter.
FIGURE 7 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 7. Images of BNHS 1987 Ahaetulla nasuta. (a) Head lateral. (b) Head dorsal. (c) Ventral. Images of a live, uncollected individual from Sri Lanka A. nasuta. (d) Head lateral. (e) Head dorsal. (f) Ventral (Images a & b to scale, other images not to scale).
FIGURE 2 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 2. PCA plot shows quantitative morphological space shared by Ahaetulla spp.. In the figure, members of the Ahaetulla nasuta species complex with lineages L3—A. borealis sp. nov. (dark blue crosses), L4—A. farnsworthi sp. nov. (green filled squares), L5—A. isabellina comb. nov. (indigo cross) and L6—A. malabarica sp. nov. (blue squares) from the Western Ghats are clustered together and share morphological space with the arid area populations L1—A. oxyrhyncha comb. nov. (circle), L7—A. sahyadrensis nom. nov. and A. anomala (indicated by a black dot). The PCA plots correspond to the scores and loadings presented in Appendix IV (A, B & C)
FIGURE 11 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 11. Images of Ahaetulla sahyadrensis nom. nov. Images of BNHS2015. (a) Head dorsal. (b) Head lateral. (c) Section of body and ventrals. (d–f) Everted Hemipenis. (g) Full specimen. Images of live, uncollected individuals, (h) Near Jog falls, Karnataka, (i) from Agumbe, (j) Kudhremukh, (k) from Agumbe (Images a & b; d, e & f to scale, other images not to scale).
FIGURE 12 in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 12. Images of Ahaetulla pulverulenta, Sri Lanka. (a) Head dorsal, (b) Head lateral, (c) Whole animal (images not to scale).
Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
Recent research has shown that the helmeted terrapin (Pelomedusa subrufa), a species that occurs throughout sub-Saharan Africa, in Madagascar and the southwestern Arabian Peninsula, consists of several deeply divergent genetic lineages. Here we examine all nominal taxa currently synonymized with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA sequences of type specimens or topotypic material for most taxa. Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray, 1863, Pelomedusa galeata var. disjuncta Vaillant & Grandidier, 1910, and Pelomedusa galeata damarensis Hewitt, 1935. For Pelomedusa gasconi Rochebrune, 1884, a taxon without preserved type material, a neotype is designated. Type material of Pentonix americana Cornalia, 1849, a nominal species without credible type locality, is lost and its identity remains questionable. Also the holotype of Pelomedusa galeata orangensis Hewitt, 1935 is lost, but its allocation to the only genetic lineage occurring in South Africa is unambiguous. Phylogenetic analyses of type sequences or topotypic material reveal that the remaining nominal taxa represent three of the nine previously identified lineages of Pelomedusa. Among these three lineages is the South African one. Type specimens of Pentonyx gehafie Rüppell, 1835 correspond to an additional distinct lineage. The present study provides a sound basis for a subsequent integrative taxonomic revision of the Pelomedusa complex.
Data from: Disentangling the effect of competition, CO2 and climate on intrinsic water-use efficiency and tree growth
1. Climate change scenarios forecast rising temperatures for the Mediterranean region, which could enhance vulnerability to drought stress in forest ecosystems. The long-term effects of climate forcing on tree performance can be, however, modulated by other environmental factors, such as competition and rising atmospheric CO2 concentrations. 2. We assessed the concomitant effect of competition, climate and CO2 concentrations on the tree-ring δ13C-derived intrinsic water-use efficiency (iWUE) and basal area increments (BAI) of species with different drought tolerance: two Mediterranean deciduous species (Quercus faginea Lam. and Quercus pyrenaica Willd.) and one conifer (Pinus sylvestris L.). Additionally, given that competition may be managed to mitigate the effect of increasing drought stress, we further examined the influence of this variable on iWUE and growth using data compiled from the literature, providing the first review on the response of iWUE to competition. 3. Competition had no significant effect on iWUE in any of the three species studied, whereas, as expected, growth rates were significantly higher under low competition levels. This was consistent with the literature review, which showed that shifts in iWUE with competition changes are rare; supporting the hypothesis that leaf-level gas exchange tends to be a homeostatic trait. In the long term, the three species exhibited a significant increasing trend in iWUE due to the combined effect of increased CO2 concentration, climate and age. Growth, however, was mostly affected by competition and climate and in most cases was not enhanced as a result of the increase in iWUE. 4. Synthesis. Regardless of their functional response to drought, trees respond to reduced competition through structural shifts such as increased radial growth rather than leaf-level gas exchange adjustments. CO2 and climate are, therefore, the main drivers of iWUE variability, rather than competition. Thus, if temperature-induced drought becomes limiting, reducing competition for resources may not offset the detrimental effect of increasing drought stress on tree physiology and growth decline may occur without a CO2 fertilization effect.
Data from: Crown asymmetry in high latitude forests: disentangling the directional effects of tree competition and solar radiation
Light foraging by trees is a fundamental process shaping forest communities. In heterogeneous light environments this behavior is expressed as plasticity of tree growth and the development of structural asymmetries. We studied the relative influence of neighborhood structure and directional solar radiation on horizontal asymmetry of tree crowns in late-successional high latitude (67–68°N) forests in northern Fennoscandia. We described crown asymmetries as crown vectors (i.e. horizontal vectors from stem center to crown center), which we obtained from canopy maps based on crown perimeter measurements in the field. To disentangle the influence of the two main determinants, inter-tree competition and directionality of above-canopy solar radiation at high latitudes, we applied circular statistical models, utilizing cylindrical distributions, to these data consisting of orientations and intensities of crown asymmetry. At the individual tree level, our model predicted crown asymmetry vectors from the current stand structure, and the predictions became better when the intensity of asymmetry (i.e. crown vector length) was higher. Competition was the main determinant of crown asymmetry for 2/3 of trees, and the model predictions improved when we incorporated the directionality of solar radiation. At the stand-level, these asymmetries had resulted in a small increment of the projected canopy area and an increased regularity of spatial structure. Our circular statistical modelling approach provided a quantitative evaluation of the relative importance of directionality of solar radiation and neighborhood stand structure, showing how both of these factors play a role in formation of crown asymmetries in high latitude forests. This approach further demonstrated the applicability of circular statistical modeling in ecological studies where the response variable has both orientation and intensity.
Data from: Disentangling species limits in the Vauquelinia corymbosa complex (Pyreae, Rosaceae)
Vauquelinia corymbosa (Pyreae, Rosaceae) is a shrubby sclerophyllous species largely restricted to the Chihuahuan Desert, distributed from Texas, Coahuila, and along the Sierra Madre Oriental to Hidalgo. According to a previous taxonomic revision, it comprises six subspecies. Vauquelinia corymbosa has noteworthy morphological variation, mostly in leaf characters, and the majority of its subspecies are restricted to certain areas of the desert. In this study, based on 16 morphometric characters and four anatomical characters collected from 201 specimens of the six subspecies throughout their distribution range,we ran a number of uni-, multivariate, and phylogenetic analyses to determine how many species can be recognized in this species complex. We also analyzed the gaps in morphology across geography to identify whether gaps in morphometric characters are indeed useful to separate species or if they are the result of variation related to geography. The results of the analyses coincided in recognizing that subsp. angustifolia should be considered a separate species and that the remaining subspecies are part of Vauquelinia corymbosa with remarkable morphological variation. Vauquelinia angustifolia has diagnostic characters such as very narrow leaves (0.4–0.6 cm at the middle and 0.2–0.4 cm at the base) and short petioles (1–1.5 cm) and it is restricted to the northeastern region of the Chihuahuan Desert.
Data from: Disentangling plastic and genetic changes in body mass of Siberian jays
Spatial and temporal phenotypic differentiation in mean body size is of commonplace occurrence, but the underlying causes remain often unclear: both genetic differentiation in response to selection (or drift) and environmentally induced plasticity can create similar phenotypic patterns. Studying changes in body mass in Siberian jays (Perisoreus infaustus) over three decades, we discovered that mean body mass declined drastically (ca. 10%) over the first two decades, but increased markedly thereafter back to almost the initial level. Quantitative genetic analyses revealed that although body mass was heritable (h2 = 0.46), the pronounced temporal decrease in body mass was mainly a product of phenotypic plasticity. However, a concomitant and statistically significant decrease in predicted breeding values suggests a genetic component to this change. The subsequent increase in mean body mass was indicated to be entirely due to plasticity. Selection on body mass was estimated to be too weak to fully account for the observed genetic decline in body mass, but bias in selection differential estimates due to environmental covariance between body mass and fitness is possible. Hence, the observed body mass changes appear to be driven mainly by phenotypic plasticity. Although we were not able to identify the ecological driver of the observed plastic changes, the results highlight the utility of quantitative genetic approaches in disentangling genetic and phenotypic changes in natural populations.
Data from: Next-generation museomics disentangles one of the largest primate radiations
Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA dataset from museum specimens, we document how NGS technologies can 'unlock' museum collections, thereby helping to unravel the tree-of-life.
Data from: Reconstructing hyperdiverse food webs: gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs
1. Anthropogenic stressors have strong impacts on ecosystems. To understand their influence, detailed knowledge about trophic relationships among species is critical. However, this requires both exceptional resolution in dietary assessments and sampling breadth within communities, especially for highly-diverse, tropical ecosystems. 2. We used gut content metabarcoding across a broad range of coral reef fishes (8 families, 22 species) in Mo'orea, French Polynesia to test whether this technique has the potential to capture the structure of a hyperdiverse marine food web. Moreover, we explored whether taxonomic groups (families) and traditional, broad-scale trophic assignments explained fish diet across four different metrics of quantifying predator-prey interactions. 3. Metabarcoding yielded a large number (4,341) of unique operational taxonomic units (i.e. prey) with high-resolution taxonomic assignments (i.e. often to the level of genus or species). We demonstrate that across multiple metrics, taxonomic group at the family level is a consistently better, albeit still weak, predictor of empirical trophic relationships than frequently-used, broad-scale functional assignments. Our method also reveals a complex trophic network with fine-scale partitioning among species, further emphasizing the importance of examining fish diets beyond broad trophic categories. 4. We demonstrate the capacity of metabarcoding to reconstruct diverse and complex food webs with exceptional resolution, a significant advancement from traditional food web reconstruction. Further, this method allows us to pinpoint the trophic niche of species with niche-based modelling, even across hyperdiverse species assemblages such as coral reefs. In conjunction with complementary techniques such as stable isotope analysis, applying metabarcoding to whole communities will provide unparalleled information about energy and nutrient fluxes and inform their susceptibility to disturbances even in the world's most diverse ecosystems.
Data from: Disentangling drivers of the abundance of coral reef fishes in the Western Indian Ocean
Aim: Understanding the drivers of the structure of coral reef fish assemblages is vital for their future conservation. Quantifying the separate roles of natural drivers from the increasing influence of anthropogenic factors, such as fishing and climate change, is a key component of this understanding. It follows that the intrinsic role of historical biogeographical and geomorphological factors must be accounted for when trying to understand the effects of contemporary disturbances such as fishing. Location: Comoros, Madagascar, Mozambique and Tanzania, western Indian Ocean (WIO). Methods: We modelled patterns in the density and biomass of an assemblage of reef-associated fish species from 11 families, and their association with 16 bio-physical variables. Results: Canonical Analysis of Principal Coordinates revealed strong country affiliations of reef fish assemblages and distance-based linear modelling confirmed geographic location and reef geomorphology were the most significant correlates, explaining 32% of the observed variation in fish assemblage structure. Another 6-8% of variation was explained by productivity gradients (chl_a), and reef exposure or slope. Where spatial effects were not significant between mainland continental locations, fishing effects became evident explaining 6% of the variation in data. No correlation with live coral was detected. Only 37 species, predominantly lower trophic level taxa, were significant in explaining differences in assemblages between sites. Main Conclusions: Spatial and geomorphological histories remain a major influence on the structure of reef fish assemblages in the WIO. Reef geomorphology was closely linked to standing biomass, with 'ocean-exposed' fringing reefs supporting high average biomass of ~1,000 kg/ha, while 'lagoon-exposed fringing' reefs and 'inner seas patch complex' reefs yielded substantially less at ~500kg/ha. Further, the results indicate the influence of benthic communities on fish assemblages is scale dependent. Such insights will be pivotal for managers seeking to balance long-term sustainability of artisanal reef fisheries with conservation of coral reef systems.
Disentangling the coexistence strategies of mud-daubing wasp species through trophic analysis in oases of Baja California peninsula
<p>Species within the same trophic level show different strategies to avoid competition. Among these mechanisms, differences in body size, spatio-temporal segregation, and diet preference often leads to a niche partitioning. Nonetheless, little attention on coexisting predatory insects and their network interactions has been paid. In this study, we analyzed the strategies to avoid competition among three sympatric mud-daubing wasps of the genus <i>Trypoxylon </i>(Hymenoptera: Crabronidae) in oases and their surrounding xeric area from the Baja California peninsula, Mexico. We compared the prey richness, composition and proportion of spider guilds that were captured by the wasps. We tested whether the differences in wasp body size explained the niche breadth, niche overlap and the size of spider prey. We assessed the spider-wasp interactions through a network analysis. With the use of trap-nests, we collected 52 spider species captured by the wasps. Both the guild and species composition of preyed spiders was different between the three wasp species. Differential proportions in the capture of spider guilds and a little diet overlap were found among the wasp species. We found that the wasp body size was positively correlated with prey size, but it was not a <i>proxy </i>of niche breadth. Moreover, the largest wasp species was able to nest in both mesic and xeric habitats, while the two smaller species were restricted to the oases. This study reveals that the diversity of spiders in oases of Baja California peninsula is crucial to maintain highly specialized oasis-dependent wasp species. The niche partitioning between mud-daubing wasps can be shaped by their inherent body size limitations and hunting strategies through foraging specialization for specific spider guilds. Food selection and slight differences in body size reduce competition and allow the coexistence of sympatric wasps. Our study is the first approach exploring the interaction networks between mud-daubing wasps and their spider preys, highlighting new insights into the morphological and ecological factors that shape antagonistic interactions, and allow the coexistence of predators in deserts.</p>
Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation". Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated chromosome rearrangements. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, chromosome rearrangements impact multiple cellular processes and these effects need to be considered together, along with those of genic divergence. Understanding the effects of chromosome rearrangements together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
Data from: Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae)
The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water-impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank-forming lineages compared to tank-less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.
Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers
Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds that were color matched and cast using scent-free surgical silicone, to which we could add scent. We used GC-MS to measure scents in co-occurring mushrooms, and related orchids, and used these scents in field experiments. By combining silicone flower parts with real floral organs, we created chimeras that identified the mushroom-like labellum as a source of volatile attraction. In addition, we showed remarkable overlap in the volatile chemistry between D. lafleurii and co-occurring mushrooms. The characters defining the genus Dracula – a mushroom-like, 'gilled' labellum and a showy, patterned calyx – enhance pollinator attraction by exploiting the visual and chemosensory perceptual biases of drosophilid flies. Our techniques for the manipulation of complex traits in a nonmodel system not conducive to gene silencing or selective breeding are useful for other systems.
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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.