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389 results for “ancestral”
Data from: Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)
<p>Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus <i>Erysimum</i> (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of <i>E. cheiranthoides</i> and foliar transcriptomes of 47 additional <i>Erysimum</i> species to construct a phylogeny from 9,869 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in <i>Erysimum</i> thus appear to provide complementary rather than redundant functions.</p>
Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.
Data from: Survival relative to new and ancestral host plants, phytoplasma infection and genetic constitution in host races of a polyphagous insect disease vector
Dissemination of vectorborne diseases depends strongly on the vector's host range and the pathogen's reservoir range. Because vectors interact with pathogens, the direction and strength of a vector's host shift is vital for understanding epidemiology and is embedded in the framework of ecological specialization. This study investigates survival in host-race evolution of a polyphagous insect disease vector, Hyalesthes obsoletus, whether survival is related to the direction of the host shift (from field bindweed to stinging nettle), the interaction with plant-specific strains of obligate vectored pathogens/symbionts (stolbur phytoplasma), and whether survival is related to genetic differentiation between the host races. We used a twice repeated, identical nested experimental design to study survival of the vector on alternative hosts and relative to infection status. Survival was tested with Kaplan–Meier analyses, while genetic differentiation between vector populations was quantified with microsatellite allele frequencies. We found significant direct effects of host plant (reduced survival on wrong hosts) and sex (males survive longer than females) in both host races and relative effects of host (nettle animals more affected than bindweed animals) and sex (males more affected than females). Survival of bindweed animals was significantly higher on symptomatic than nonsymptomatic field bindweed, but in the second experiment only. Infection potentially had a positive effect on survival in nettle animals but due to low infection rates the results remain suggestive. Genetic differentiation was not related to survival. Greater negative plant-transfer effect but no negative effect of stolbur in the derived host race suggests preadaptation to the new pathogen/symbiont strain before strong diversifying selection during the specialization process. Physiological maladaptation or failure to accept the ancestral plant will have similar consequences, namely positive assortative mating within host races and a reduction in the likelihood of oviposition on the alternative plant and thus the acquisition of alternative stolbur strains.
Data from: Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America
The hawkmoth genus Manduca is a diverse group of very large, conspicuous moths that has served as an important model across many biological disciplines. Two species in particular, the tobacco hornworm (Manduca sexta) and the tomato hornworm (Manduca quinquemaculatus) have been researched extensively. Studies across biological fields have referred to these two species as being closely related or even sister species, but the extent to which these two model organisms are related remains largely unknown. We conducted a comprehensive multi-gene phylogenetic analysis of Manduca, based on both an ML and Bayesian framework, which resulted in a monophyletic Manduca but only when two other genera, Dolba and Euryglottis are included. We tentatively conclude that the sister group to Manduca sexta comprises the Caribbean M. afflicta and M. johanni, and the sister lineage to this clade includes M. quinquemaculatus and the Hawaiian M. blackburni. Thus, M. sexta and M. quinquemaculatus are closely related, but are not sister species. Biogeographical analyses reveal an ancestral center of diversification in Central America, and Manduca appears to have subsequently colonized North and South America. Our phylogeny provides an important foundation for comparative studies of two model organisms and their relatives.
Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification
The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
If an ancestral stem group repeatedly colonizes similar environments, developmental plasticity specific to that group should consistently give rise to similar phenotypes. Parallel selection on those similar phenotypes could lead to the repeated evolution of characteristic ecotypes, a property common to many adaptive radiations. A key prediction of this "flexible stem" model of adaptive radiation is that patterns of phenotypic divergence in derived groups should mirror patterns of developmental plasticity in their common ancestor. The threespine stickleback radiation provides an excellent opportunity to test this prediction because the marine form is representative of the ancestral stem group, which has repeatedly given rise to several characteristic ecotypes. We examined plasticity of several aspects of shape and trophic morphology in response to diets characteristic of either the derived benthic or limnetic ecotypes. When marine fish were reared on alternative diets, plasticity of head and mouth shape paralleled phenotypic divergence between the derived ecotypes, supporting the flexible stem model. Benthic and limnetic fish exhibited patterns of plasticity similar to the marine population; however, some differences in population means were present, as well as subtle differences in shape plasticity in the benthic population, indicating a role for genetic accommodation in this system.
Data from: Trpc2 Pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss
Comparative methods are often used to infer loss or gain of complex phenotypes, but few studies take advantage of genes tightly linked with complex traits to test for shifts in the strength of selection. In mammals vomerolfaction detects chemical cues mediating many social and reproductive behaviors and is highly conserved, but all bats exhibit degraded vomeronasal structures with the exception of two families (Phyllostomidae and Miniopteridae). These families either regained vomerolfaction after ancestral loss, or there were many independent losses after diversification from an ancestor with functional vomerolfaction. In this study, we use the Transient receptor potential cation channel 2 (Trpc2) as a molecular marker for testing the evolutionary mechanisms of loss and gain of the mammalian vomeronasal system. We sequenced Trpc2 exon 2 in over 100 bat species across 17 of 20 chiropteran families. Most families showed independent pseudogenizing mutations in Trpc2, but the reading frame was highly conserved in phyllostomids and miniopterids. Phylogeny-based simulations suggest loss of function occurred after bat families diverged, and purifying selection in two families has persisted since bats shared a common ancestor. As most bats still display pheromone-mediated behavior, they might detect pheromones through the main olfactory system without using the Trpc2 signaling mechanism.
Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates
<p>Pinopsin is the opsin most closely related to vertebrate visual pigments on the phylogenetic tree. This opsin has been discovered among many vertebrates, except mammals and teleosts, and was thought to exclusively function in their brain for extraocular photoreception. Here, we show the possibility that pinopsin also contributes to scotopic vision in some vertebrate species. Pinopsin is distributed in the retina of non-teleost fishes and frogs, especially in their rod photoreceptor cells, in addition to their brain. Moreover, the retinal chromophore of pinopsin exhibits a thermal isomerization rate considerably lower than those of cone visual pigments, but comparable to that of rhodopsin. Therefore, pinopsin can function as a rhodopsin-like visual pigment in the retinas of these lower vertebrates. Since pinopsin diversified before the branching of rhodopsin on the phylogenetic tree, two-step adaptation to scotopic vision would have occurred through the independent acquisition of pinopsin and rhodopsin by the vertebrate lineage.</p>
Data from: Oldest known multituberculate stapes suggests an asymmetric bicrural pattern as ancestral for Multituberculata
Middle ear ossicles (malleus, incus, stapes) are known only for few multituberculate taxa, and three different stapedial morphotypes have been suggested: (1) slender, columelliform and microperforate, (2) robust and rod-like, and (3) bicrural. Reinvestigation of Upper Jurassic (Kimmeridgian) mammalian petrosals from the Guimarota coal mine in central Portugal (Western Europe) revealed an asymmetric bicrural stapes (ABS) in the paulchoffatiid Pseudobolodon oreas. The middle ear bones displaced inside the osseous vestibule were detected by a microCT analysis. The Kimmeridgian age of the Guimarota stapes exceeds the stapes from the Early Cretaceous (Barremian) of Asia (about 122-124 ma) by ~30 ma, and is only slightly younger than the stapes of the recently described Oxfordian euharamiyid Arboroharamiya allinhopsoni. The Guimarota stapes indicates that the stapes of Lambdopsalis, described as columelliform and microperforate (small stapedial foramen), does not represent a general condition for multituberculates. The stapes of Pseudobolodon is bicrural, the anterior crus sits centrally on the oval footplate, and the stapedial head is simple and smaller than the footplate. We hypothesize that the ABS evolved from the symmetric bicrural stapes (SBS) of non-mammaliaform cynodonts. The ABS appears to be the ancestral morphotype of the mammalian SBS, and the mammalian columelliform imperforate stapes (CIS).
FIGURE 1. Ancestral character-state reconstructions for Characters 1–9 in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing
FIGURE 1. Ancestral character-state reconstructions for Characters 1–9. Ambiguities in Macrogenioglottus alipioi and Odontophrynus carvalhoi in Characters 5–7 are due to polymorphism.
Figure 2 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 2. Bayesian consensus tree resulting from the LW-Rh and Wg gene alignments (871 bp). Coloured dots on the branches indicate the values of posterior probability (PP): green dots represent values between 1.00 and 0.95, yellow dots between 0.94 and 0.90, and red dots ≤ 0.89. The nodes are indicated with numbers. Values above and below the branches represent the ancestral genome size (GS; 1C-values, in picograms) at particular nodes: in blue is the value generated by the maximum likelihood (ML) [asterisks are related to confidence interval (CI) values shown in Supporting Information, Table S4]; orange is the value generated by maximum parsimony (MP); and black, given below the branches, is the value generated by Bayesian inference (BI). Genome size data (1C-values) were obtained in the present work (pink dots) or taken from the literature (grey dots).
Figure 1 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 1. Fluorescence intensity histograms obtained from three different species, with Drosophila melanogaster as internal standard, stained with propidium iodide (PI; A–C) or 4,6-diamidino-2-phenylindole (DAPI; D–F). The x-axis corresponds to the scale of fluorescence intensity, and the y-axis represents the number of nuclei with that fluorescence intensity.
Figure 3 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 3. Mean genome size (in picograms and megabase pairs) estimated for Formicidae subfamilies. The phylogenetic tree generated in the present study was redrawn, with collapsed branches corresponding to species of the same subfamily.
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S-DIVA algorithm using ultrametric COI tree calculated in BEAST 2.4 software. Numbers at the tips of the trees correspond to the sampling locations on the map (designated as in Fig. 1). Letters represent most likely ancestral range. Sectors in circles indicate the percent of total range probability. Biogeographical regions in the map as in Piepenburg et al. (2011), Ekimova et al. (2019), Laakkonen et al. (2021).
Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions
<p>Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral dinosaurian features<span> </span>(e.g., forward-facing pubis, short ilium, pubic 'boot') are transiently present in the early morphogenesis of birds and arrive at their typical 'avian' form after transitioning through a prenatal developmental sequence that mirrors phylogeny. We quantitatively demonstrate that avian pelvic ontogeny closely parallels the dinosaur-to-avian transition and provide evidence for an evolutionary module within the pelvis that is conserved across Archosauria. The presence of ancestral states in avian embryos may stem from this conserved modular relationship. These are further indications that the avian pelvis evolved via terminal addition—a mechanism whereby ancestral states shift to derived states during late development, resulting in retention of ancestral character states. This phenotypic modularity suggests a previously unrecognized mechanism for the promotion of terminal addition, hinting that the retention of ancestral states in development may be common across evolutionary transitions.</p>
Data from: Schneider et al. (2021). Predominantly eastward long-distance dispersal in pantropical Ochnaceae inferred from ancestral range estimation and phylogenomics. Frontiers in Ecology and Evolution.
<p>The data contains (a) DNA sequence alignments of concatenated nuclear loci, near-complete plastid genomes and plastid genomes with sites removed at a 10% gap threshold; (b) maximum clade credibility trees obtained from divergence time estimation in BEAST with each of the alignments; (c) area codings and the input tree (nuclear DNA only) for the ancestral area analysis in BioGeoBears.</p>
Data from: Ancestral ecological regime shapes reaction to food limitation in the Least Killifish, Heterandria formosa
<p>Populations with different densities often show genetically-based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per-capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food-independent factors potentially affecting density, such as predation intensity. Here we present a case study of two populations of a small live-bearing freshwater fish, one characterised by high density, low predation risk, low overall food availability, and presumably low per-capita food levels, and the other by low density, high predation risk, high overall food availability, and presumably high per-capita food levels. Using a laboratory experiment we examined whether fish from these populations respond differently to food limitation, and whether size at birth, a key trait with respect to density variation in this species, is associated with any such differential responses. While at the lower food level growth was slower, body size smaller, maturation delayed and survival reduced in both populations, these fitness costs were smaller in fish from the high-density population. At low food, only 15% of high-density fish died, compared to 75% of low-density fish. This difference was much smaller at high food (0% vs. 15% mortality). The increased survival of high-density fish may, at least partly, be due to their larger size at birth. Moreover, being larger at birth enabled fish to mature relatively early even at the lower food level. We demonstrate that sensitivities to food limitation differ between study populations, consistent with selection for a greater ability to tolerate low per-capita food availability in the high-density population. While we cannot preclude other agents of selection from operating in these populations simultaneously, our results suggest that variation in per-capita food levels is one of those agents.</p>
Earth and life evolve together from something ancestral — reply to Britz et al
<p class="MsoNormal"><span>Ricefishes of the family Adrianichthyidae are considered to have dispersed eastward "out-of-India" after the collision of the Indian subcontinent with Eurasia and subsequently diversified in Southeast<span class="s1"><span>-</span></span>East Asia. In this study, </span><span>we reconstructed ancestral areas of Adrianichthyidae with BioGeoBEARS, expanding the scope to include Cyprinodontiformes, the outgroup of Beloniformes to which Adrianichthyidae belongs. The results again supported the "out-of-India" dispersal scenario. The dataset contained all files necessary for the BioGeoBEARS analysis.</span></p>
Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny
<p>A clade's evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant ( n = 419) and extinct ( n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.</p>
Figure 6. Ancestral ranges within Magrebmelia inferred with the package BioGeoBEARS using the DEC model. Temporal estimates derived from a in The Strait of Gibraltar is an ineffective palaeogeographic barrier for some flightless darkling beetles (Coleoptera: Tenebrionidae: Pimelia)
Figure 6. Ancestral ranges within Magrebmelia inferred with the package BioGeoBEARS using the DEC model. Temporal estimates derived from a relaxed molecular clock analysis. Maximum Clade Credibility (MCC) tree showing clade divergence times in millions of years. Coloured squares represent ancestral ranges depicted in the map, upper left; A, Betic, B, Rifean/ Kabylia, C, Middle Atlas, D, High Atlas. Coloured branches correspond to arrows in the lower left maps (1, 2), which indicate diversification route of Magrebmelia throughout the western Mediterranean Basin since the Early Miocene [East lineage (red) and South lineage (purple)], based on biogeographical reconstructions of western Mediterranean Pimelia (MasPeinado et al., 2018). Populations morphologically assignable to P. xauenensis but related to P. mauritanica are indicated by specimen numbers. Maps 1–2 modified from Andeweg (2002); Meulenkamp & Sissingh (2003).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.