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FIGURE 1 in Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China
FIGURE 1. Phylogenetic tree of Comatricha (based on SSU) which shows relationships among species in this genus along with species in the genera Meriderma, Lamproderma, Stemonitopsis and Diacheopsis. New species are indicated in bold and red colour. Support in nodes is indicated when posterior probabilities are>95%.
FIGURE 4 in Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China
FIGURE 4. Comatricha afroalpina Rammeloo (HMJAU: M1006) A. Sporocarps occurring on a log; B. Two sporocarps as observed by SEM; C. Incomplete surface net and spores as observed by SEM; D. A portion of the spores and capillitium as viewded by TL; E-F. Spores marked with warts by as viewed by SEM. (Bar: A=1 mm)
FIGURE 3 in Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China
FIGURE 3. Comatricha tenerrima (M.A. Curtis) G. Lister (HMJAU: M1058) A. Sporocarp as observed by SEM; B-D. Capillitium and spores as observed by SEM and TL; E-F. Spores marked with warts as viewed by SEM.
FIGURE 2 in Identification of the new species Comatricha macrospora and two other recently recorded species of Comatricha from China
FIGURE 2.. Comatricha macrospora B. Zhang & Yu Li (HMJAU-M1066!) A. Sporocarp growing on a log; B. Sporocarp as seen by SEM, C. Columella and capillitia; D. Capillitia and spores as seen by TL; E. Peridia and capillitia; F. Spores marked with spines. (Bar: A = 2 mm)
FIGURE 1. Vellozia pyrantha. A. Habit with marcescent and reflexed leaves without recent fire influence. B. Habit after fire and flowering. C. Orange flammable resin. D. Flowers. E. Tepal with three stamens. F. Ovary, transversal cut. G–H. Ovary, longitudinal cut. I–M. Fruits morphology variation. K. Apical slits showing seeds inside the fruit. L in Old for people, new for science: a previously undescribed species of harvested Vellozia (Velloziaceae) endemic to the Chapada Diamantina National Park, Bahia (Brazil)
FIGURE 1. Vellozia pyrantha. A. Habit with marcescent and reflexed leaves without recent fire influence. B. Habit after fire and flowering. C. Orange flammable resin. D. Flowers. E. Tepal with three stamens. F. Ovary, transversal cut. G–H. Ovary, longitudinal cut. I–M. Fruits morphology variation. K. Apical slits showing seeds inside the fruit. L. Longer fruits in population of Morro dos Ventos. N. Seeds.
Data and code for: Recently established predators rewire food webs simplified by extinction
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Recent ice-contact delta formation in front of Pio XI glacier controls sedimentary processes in Eyre Fjord, Patagonia
<p><span>Data for "Recent ice-contact delta formation in front of Pio XI glacier controls sedimentary processes in Eyre Fjord, Patagonia"</span></p>
FIGURE 4 in Geographical distribution of Dyckia walteriana (Bromeliaceae), a recently described and endangered species endemic to the Serra Geral formation, southern Brazil
FIGURE 4. Geographic distribution of population 10 of Dyckia walteriana in the Serra Geral formation, Paraná State, Brazil. Red area: registered population (yellow square B in Figure 2).
FIGURE 3 in Geographical distribution of Dyckia walteriana (Bromeliaceae), a recently described and endangered species endemic to the Serra Geral formation, southern Brazil
FIGURE 3. Geographic distribution of populations 1-9 & 12 of Dyckia walteriana in the Serra Geral formation, Paraná State, Brazil. Red areas: registered populations (yellow square A in Figure 2).
FIGURE 2 in Geographical distribution of Dyckia walteriana (Bromeliaceae), a recently described and endangered species endemic to the Serra Geral formation, southern Brazil
FIGURE 2. Geographic distribution of Dyckia walteriana in the Serra Geral formation, Paraná State, Brazil. Red polygon: region studied in order to select promising locations for the occurrence of D. walteriana populations. Yellow squares: regions of occurrence of one or more populations. A see Figure 3; B see Figure 4; C see Figure 5.
FIGURE 1 in Geographical distribution of Dyckia walteriana (Bromeliaceae), a recently described and endangered species endemic to the Serra Geral formation, southern Brazil
FIGURE 1. Some of the Dyckia walteriana populations identified in the Serra Geral formation, Paraná state, Brazil. A = population 1 (before the intentional fire); B = population 2; C = population 8; D = population 10.
FIGURE 5 in Geographical distribution of Dyckia walteriana (Bromeliaceae), a recently described and endangered species endemic to the Serra Geral formation, southern Brazil
FIGURE 5. Geographic distribution of population 11 of Dyckia walteriana in the Serra Geral formation, Paraná State, Brazil. Red area: registered population (yellow square C in Figure 2).
FIGURE 1 in Lectotype of Solidago ×niederederi (Asteraceae) selected from a recently rediscovered original material
FIGURE 1. The lectotype specimen of Solidago ×niederederi mounted on two herbarium sheets (A—PRC455790, B—PRC455791) deposited in the PRC herbarium.
CAMI2 Challenge - Human Microbiome Project Toy Database - sample 19 - regenerated using recent RefSeq representative genomes
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Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as sub-fossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established Maximum Likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a 'crown-giant' ecomorph anole hypothesized to have once been found throughout the Spanish, U.S., and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.
Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.
A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona priniceps) from the sky islands of the central Rocky Mountains of North America are used to provide insights into key questions about integrative approaches in landscape genetics, population genetics and phylogeography. This includes (i) general issues surrounding the conversion of time-specific SDMs into simple continuous, dynamic landscapes from past to current, and (ii) the utility of SDMs to inform demographic models with deme-specific carrying capacities and migration potentials, as well as (iii) the contribution of the temporal dynamic of colonization history in shaping genetic patterns of contemporary populations. Our results support that the inclusion of a spatiotemporal dynamic is an important factor when studying the impact of distributional shifts on patterns of genetic data. Our results also demonstrate the utility of SDMs to generate species-specific predictions about patterns of genetic variation that account for varying degrees of habitat specialization and life-history characteristics of taxa. Nevertheless, the results highlight some key issues when converting SDMs for use in demographic models. Because the transformations have direct affects on the genetic consequence of population expansion by prescribing how habitat heterogeneity and spatiotemporal variation is related to the species-specific demographic model, it is important to consider alternative transformations when studying the genetic consequences of distributional shifts.
Data from: Malaria infections reinforce competitive asymmetry between two Ficedula flycatchers in a recent contact zone
Parasites may influence the outcome of interspecific competition between closely related host species through lower parasite virulence in the host with which they share the longer evolutionary history. We tested this idea by comparing the prevalence of avian malaria (Haemosporidia) lineages and their association with survival in pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breeding in a recent contact zone on the Swedish island of Öland. A nested PCR protocol amplifying haemosporidian fragments of mtDNA was used to screen the presence of malaria lineages in 1048 blood samples collected during 6 years. Competitively inferior pied flycatchers had a higher prevalence of blood parasites, including the lineages that were shared between the two flycatcher species. Multistate mark–recapture models revealed a lower survival of infected versus uninfected female pied flycatchers, while no such effects were detected in male pied flycatchers or in collared flycatchers of either sex. Our results show that a comparatively new host, the collared flycatcher, appears to be less susceptible to a local northern European malarial lineage where the collared flycatchers have recently expanded their distribution. Pied flycatchers experience strong reproductive interference from collared flycatchers, and the additional impact of species-specific blood parasite effects adds to this competitive exclusion. These results support the idea that parasites can strongly influence the outcome of interspecific competition between closely related host species, but that the invading species need not necessarily be more susceptible to local parasites.
Data from: Recent speciation between sympatric Tanganyikan cichlid color morphs
Lake Tanganyika, Africa's oldest lake, harbors an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric color morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid color morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances, and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.
Data from: Contemporary ecotypic divergence during a recent range expansion was facilitated by adaptive introgression
Although rapid phenotypic evolution during range expansion associated with colonization of contrasting habitats has been documented in several taxa, the evolutionary mechanisms that underlie such phenotypic divergence have less often been investigated. A strong candidate for rapid ecotype formation within an invaded range is the three-spine stickleback in the Lake Geneva region of central Europe. Since its introduction only about 140 years ago, it has undergone a significant expansion of its range and its niche, now forming phenotypically differentiated parapatric ecotypes that occupy either the pelagic zone of the large lake or small inlet streams, respectively. By comparing museum collections from different times with contemporary population samples, we here reconstruct the evolution of parapatric phenotypic divergence through time. Using genetic data from modern samples, we infer the underlying invasion history. We find that parapatric habitat-dependent phenotypic divergence between the lake and stream was already present in the first half of the twentieth century, but the magnitude of differentiation increased through time, particularly in antipredator defence traits. This suggests that divergent selection between the habitats occurred and was stable through much of the time since colonization. Recently, increased phenotypic differentiation in antipredator defence traits likely results from habitat-dependent selection on alleles that arrived through introgression from a distantly related lineage from outside the Lake Geneva region. This illustrates how hybridization can quickly promote phenotypic divergence in a system where adaptation from standing genetic variation was constrained.
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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.