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Data from: A redescription and phylogenetic analysis based on new material of the fossil newts Taricha oligocenica Van Frank, 1955 and Taricha lindoei Naylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon.
Complete body fossils of salamanders are relatively rare, but provide critical information on the evolutionary roots of extant urodele clades. We describe new specimens of the fossil salamandrids Taricha oligocenica Van Frank, 1955, and Taricha lindoei Naylor, 1979, from the Oligocene Mehama and John Day Formations of Oregon that illustrate aspects of skeletal morphology previously unseen in these taxa, and contribute to our understanding of population-level variation. Morphological analysis of these specimens supports the classification of T. oligocenica and T. lindoei as two different species, distinct from extant Taricha. Parsimony-based, heuristic analysis of phylogeny using 108 morphological characters for 40 taxa yields different results from a phylogenetic analysis that excludes four taxa known only via vertebrae. Our smaller analysis generally agrees with molecular phylogenies of the family Salamandridae, but with poorer resolution for molgin newts, especially between Taricha and Notophthalmus. The analysis including all taxa produced polytomies mostly related to complications from several fossil taxa. The presence or absence of dorsally expanded, sculptured neural spine tables on trunk vertebrae, an important character in past descriptions of fossil salamandrids, appears to be either homoplastic within the Salamandridae, or requires an expansion of characters or character states. T. oligocenica and T. lindoei are separate species of an at least 33 million-year-old clade, but their relationships with each other and extant North American salamandrids remain unclear with current levels of morphological data. Salamandrid research requires additional morphological data, particularly for the vertebrae and ribs, to better resolve salamandrid evolutionary history through morphological characters.
Data from: Herteliana schuyleriana (Squamarinaceae), a new crustose lichen widespread in the Appalachian Mountains of eastern North America
Herteliana schuyleriana is described as new to science based on collections from throughout the Appalachian Mountains of eastern North America. Taxonomic placement is inferred from molecular phylogenic analysis of mtSSU sequence data that recovered the taxon as sister to the type species of Herteliana, H. gagei, and strongly supported these taxa as embedded within the Squamarinaceae. The new species is characterized by its occurrence on non-calcareous shaded rocks in inland forested habitats (vs. exposed maritime oceanic habitats), its greenish-blue crustose thallus, presence of abundant blastidia on the thallus surface, frequent sterility, and by the production of roccellic/angardianic acid together with occasional trace amounts of psoromic acid as accessories to atranorin.
Data from: A view from above: A view from above: unmanned aerial vehicles (UAVs) provide a new tool for assessing liana infestation in tropical forest canopies
1. Tropical forests store and sequester large quantities of carbon, mitigating climate change. Lianas (woody vines) are important tropical forest components, most conspicuous in the canopy. Lianas reduce forest carbon uptake and their recent increase may, therefore, limit forest carbon storage with global consequences for climate change. Liana infestation of tree crowns is traditionally assessed from the ground, which is labour-intensive and difficult, particularly for upper canopy layers. 2. We used a light-weight unmanned aerial vehicle (UAV) to assess liana infestation of tree canopies from above. We used a commercially available quadcopter UAV with an integrated, standard three-waveband camera to collect aerial image data for 150ha of tropical forest canopy. By visually interpreting the images, we assessed the degree of liana infestation for 14.15ha of forest for which ground-based estimates were collected simultaneously. We compared the UAV liana infestation estimates with those from the ground to determine the validity, strengths and weaknesses of using UAVs as a new method for assessing liana infestation of tree canopies. 3. Estimates of liana infestation from UAV correlated strongly with ground-based surveys at individual tree and plot level, and across multiple forest types and spatial resolutions, improving liana infestation assessment for upper canopy layers. Importantly, UAV-based surveys, including the image collection, processing and visual interpretation, were considerably faster and more cost-efficient than ground-based surveys. 4. Synthesis and applications: UAV image data of tree canopies can be easily captured and used to assess liana infestation at least as accurately as traditional ground data. This novel method promotes reproducibility of results and quality control, and enables additional variables to be derived from the image data. It is more cost-effective, time-efficient and covers larger geographical extents than traditional ground surveys, enabling more comprehensive monitoring of changes in liana infestation over space and time. This is important for assessing liana impacts on the global carbon balance, and particularly useful for forest management where knowledge of the location and change in liana infestation can be used for tailored, targeted and effective management of tropical forests for enhanced carbon sequestration (e.g. REDD+ projects), timber concessions and forest restoration.14-Nov-2018
Data from: Markov-modulated Poisson processes as a new framework for analyzing capture-recapture data
1.Opportunistic capture-recapture data consists of observations over non-constant time-intervals and so fails to satisfy the basic assumptions of traditional capture-recapture models. Analyzing opportunistic capture-recapture data is often done by discretizing time-intervals or summarizing data, but without taking into account the continuous-time process of the state and/or the capture. 2.To deal with non-constant time-intervals, continuous-time closed capture-recapture models have been proposed by Yip et al. (1996), Hwang & Chao (2002), Schofield et al. (2017) for estimating population size. More recently, a continuous-time Cormack-Jolly-Seber model has been proposed by Fouchet et al. (2016) to reduce bias in survival rates, and a two-state process has been proposed by Choquet et al. (2017) to estimate reproduction rates and survival rates of young within a season. 3.The aim of the current study is to demonstrate how an approach based on a Markov-modulated Poisson process (MMPP) (Freed & Shepp, 1982) allows, in a similar way to a multistate model, to model opportunistic data using several states. To this end, several multistate models were rewritten as MMPP models, showing, the potential for this approach to address the ecological questions as multistate models, but using an extended data framework. In particular, it is a useful framework for dealing with data that has unordered levels of uncertainty. 4.The methods were illustrated using simulations and analysis of data on the Alpine ibex (Capraibex).
Data from: New armoured scalidophorans (Ecdysozoa, Cycloneuralia) from the Cambrian Fortunian Zhangjiagou Lagerstätte, South China
Although molecular studies estimated that cycloneuralians might have originated in the Ediacaran Period and diversified in the early Cambrian, it was not until 2014 that they were first reported from the Cambrian Fortunian Stage. To date only two species and five indeterminate forms have been described. Here, we report new three‐dimensionally phosphatized microfossils of cycloneuralians from the Fortunian Zhangjiagou Lagerstätte, South China. Two new genera and species, Qinscolex spinosus gen. et sp. nov. and Shanscolex decorus gen. et sp. nov., and Indeterminate Forms 1–7 are described and tentatively assigned to total‐group Scalidophora, greatly increasing the diversity of the Fortunian cycloneuralians. These Fortunian cycloneuralians have diverse cuticular spines, plates, and spinose sclerites of various sizes on the trunk, thus assignment of co‐occurring fragmented trunk parts or disassociated spines or sclerites to a specific species is currently impossible. Some of the Fortunian cycloneuralians might have reached a centimetre in length; they may have been temporary meiobenthos in their juvenile or younger adult stages, only joining the macrobenthos when they reached macroscopic dimensions. It is proposed that an introvert with hexaradially symmetric and internally hollow scalids might be the plesiomorphic state for cycloneuralians.
Data from: Using metagenomics to show the efficacy of forest restoration in the New Jersey Pine Barrens
The Franklin Parker Preserve within the New Jersey Pine Barrens contains 5,000 acres of wetlands habitat, including old-growth Atlantic White Cedar (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former cranberry bogs undergoing restoration into AWC forests. This study showed that the C-use efficiency was greater in the old-growth AWC soils than in soils from 8-year old mid-stage restored AWC stands, which were greater than found in soil from 4-year old AWC stands—the latter two stands being restored from long-term cranberry bogs. A metagenomic analysis of eDNA extracted from these soils showed that the C-cycle trends were associated with increases in the relative numbers of DNA sequences from several copiotrophic bacterial groups (Bacteroidetes, and Proteobacteria), complex C decomposing fungal groups ( Sordiomycetes, Mortierellales, and Thelephorales), and collembolan and formicid invertebrates. All groups are indicators of successionally more advanced soils, and critical for soil C-cycle activities. These data suggest that the restoration activities studied are enhancing critical guilds of soil biota, and increasing C-use efficiency in the soils of restored habitats, and that the use of metagenomic analysis of soil eDNA can be used in the development of assessment models for soil recovery of wetlands following restoration.
Data from: Inadvertent biological control: an Australian thrips killing an invasive New Zealand tree in California
Transport hubs of international trade and tourism are sites of unprecedented long-distance dispersal of species and novel ecological interactions. In cases of invasive plants released from their specialist natural enemies, novel interactions with both resident enemies and new arrivals can accumulate and potentially reduce weed competitiveness. I present here one dramatic example of this, where an invasive woody weed in southern California is being rapidly controlled by an accidentally introduced genus-specialist herbivorous insect. The New Zealand native shrub/small tree, Myoporum laetum, is a long-time popular ornamental plant in California and has become an invasive woody weed. In 2005, a Myoporum-specific thrips, Klambothrips myopori, was discovered (and described) in California feeding on M. laetum leaves. Several searches have failed to find K. myopori in New Zealand and a population has recently been discovered in Tasmania, Australia, feeding on Myoporum insulare. In 5 years, K. myopori has killed off about half of southern Californian M. laetum with almost all surviving individuals being gradually defoliated. Inadequate border biosecurity has resulted in inadvertent biological control, in a rapid timeframe, caused by a novel enemy. Unfortunately, K. myopori has subsequently been accidentally transported from California to Hawaii where it is now killing off Hawaiian native Myoporum sandwicense. Transport hubs can both connect weeds with natural enemies and disperse those enemies more widely.
Data from: Differentiating the evolution of female song and male-female duets in the New World blackbirds: can tropical natural history traits explain duet evolution?
Female bird song and combined vocal duets of mated pairs are both frequently associated with tropical, monogamous, sedentary natural histories. Little is known, however, about what selects for duetting behavior versus female song. Female song likely preceded duet evolution and could drive apparent relationships between duets and these natural histories. We compared the evolution of female song and male-female duets in the New World blackbirds (Icteridae) by investigating patterns of gains and losses of both traits and their relationships with breeding latitude, mating system, nesting pattern, and migratory behavior. We found that duets evolved only in lineages in which female song was likely ancestral. Both female song and duets were correlated with tropical breeding, social monogamy, territorial nesting, and sedentary behavior when all taxa were included; however, correlations between duets and these natural history traits disappeared when comparisons were limited to taxa with female song. Also, likelihood values supported stronger relationships between the natural history traits and female song than between these traits and duets. Our results suggest that the natural histories thought to favor the evolution of duetting may in fact be associated with female song and that additional selection pressures are responsible for the evolution of duets.
Data from: Energetic constraint of non-monotonic mass change during offspring growth: a general hypothesis and application of a new tool
1. Postnatal growth is an important life-history trait and can be a sensitive indicator of ecological stress. For over 50 years, monotonic (never-decreasing) growth has been viewed as the predominant trajectory of postnatal mass change in most animal species, notably among birds. However, prevailing analytical approaches and energetic constraints may limit detection of non-monotonic (or multi-phasic), determinate growth patterns, such as mass recession in birds (weight-loss prior to fledging, preceded by overshooting adult mass), which is currently believed to be restricted to few taxa. 2. Energetic surplus and shortfall are widespread conditions that can directly influence the degree of mass overshooting and recession. Thus, we hypothesize that in many species prevailing energetic constraints force mass change away from a fundamental non-monotonic trajectory to instead follow a monotonic curve. 3. We observed highly non-monotonic, mass change trajectories (overshooting adult mass by up to almost 20%) among common tern Sterna hirundo chicks, a well-studied species long-established as growing monotonically. We quantified the prevalence and magnitude of non-monotonic mass change prior to fledging for 313 common tern chicks that successfully fledged from two discrete populations in multiple years. We used a new approach for analysing non-monotonic curves to examine differences in mass change trajectories between populations under contrasting abiotic (freshwater versus saltwater) and biotic stresses (low rates of food provisioning). 4. Some degree of mass recession occurred in 73% of all study chicks. Overshooting adult mass followed by extensive mass recession was most prevalent at our freshwater colony, being detected among 34 - 38% of chicks annually. Non-monotonic trajectories were less marked in populations experiencing ecological stress and among lower quality individuals. Chicks that were provisioned at higher rates were more likely to both overshoot adult mass and experience subsequent mass recession. 5. Our results provide strong support in common terns for the hypothesis that non-monotonic trajectories are the fundamental pattern of mass change but are constrained to be monotonic under energetic shortfall. This justifies future tests of the generality of this hypothesis across a broad range of taxa. We also demonstrate a recent analytical tool that prevents routine fitting of monotonic curves without prior investigation of non-monotonic trends.
Data from: Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces
We analyzed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America super-region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kind of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Meso-America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of germplasm collections.
Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.
Data from: New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)
This study documents previously unknown taxonomic and morphological diversity among early Palaeozoic crinoids. Based on highly complete, well preserved crown material, we describe two new genera from the Ordovician and Silurian of the Baltic region (Estonia) that provide insight into two major features of the geological history of crinoids: the early evolution of the flexible clade during the Great Ordovician Biodiversification Event (GOBE), and their diversification history surrounding the end-Ordovician mass extinction. The unexpected occurrence of a highly derived sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides high-resolution temporal, taxonomic and palaeobiogeographical constraints on the origin and early evolution of the Flexibilia. The Silurian (lower Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the oldest known Silurian crinoid from Baltica and thus provides the earliest Baltic record of crinoids following the aftermath of the end-Ordovician mass extinction. A Bayesian 'fossil tip-dating' analysis implementing the fossilized birth–death process and a relaxed morphological clock model suggests that flexibles evolved c. 3 million years prior to their oldest fossil record, potentially involving an ancestor–descendant relationship (via 'budding' cladogenesis or anagenesis) with the paraphyletic cladid Cupulocrinus. The sagenocrinid subclade rapidly diverged from 'taxocrinid' grade crinoids during the final stages of the GOBE, culminating in maximal diversity among Ordovician crinoid faunas on a global scale. Remarkably, diversification patterns indicate little taxonomic turnover among flexibles across the Late Ordovician mass extinction. However, the elimination of closely related clades may have helped pave the way for their subsequent Silurian diversification and increased ecological role in post-Ordovician Palaeozoic marine communities. This study highlights the significance of studies reporting faunas from undersampled palaeogeographical regions for clade-based phylogenetic studies and improving estimates of global biodiversity through geological time.
Data from: Biodiversity inventories and conservation of the marine fishes of Bootless Bay, Papua New Guinea
BACKGROUND: The effective management and conservation of biodiversity is predicated on clearly defined conservation targets. Species number is frequently used as a metric for conservation prioritization and monitoring changes in ecosystem health. We conducted a series of synoptic surveys focusing on the fishes of the Bootless Bay region of Papua New Guinea to generate a checklist of fishes of the region. Bootless Bay lies directly south of Port Moresby, the capital of Papua New Guinea, and experiences the highest human population density of any marine area in the country. Our checklist will set a baseline against which future environmental changes can be tracked RESULTS: We generated a checklist of 488 fish species in 72 families found in Bootless Bay during a two-week sampling effort. Using incident-based methods of species estimation, we extrapolate there to be approximately 940 fish species in Bootless Bay, one of the lowest reported numbers in Papua New Guinea. CONCLUSIONS: Our data suggest that the Bootless Bay ecosystem of Papua New Guinea, while diverse in absolute terms, has lower fish biodiversity compared to other shallow marine areas within the country. These differences in faunal diversity, are most likely a combination of unequal sampling effort as well as biophysical factors within Bootless Bay compounded by historical and/or contemporary anthropogenic disturbances.
Data from: Chryselium, a new South American genus segregated from Helichrysum (Asteraceae, Gnaphalieae)
Chryselium Urtubey & S. E. Freire, a new monotypic genus, is here described and illustrated to accomodate one species that was initially placed in Helichrysum, H. gnaphalioides, as Chryselium gnaphalioides . The new genus, Chryselium , is a monoecious herb with single stems and terminal capitulescences that are densely glomerulate from the Tropical Andes of Venezuela, Colombia, Ecuador, Bolivia, and Peru. This genus differs fundamentally from Helichrysum by having a stoloniferous habit and corollas with purple apices. A molecular analysis using DNA sequences from nuclear (ITS and ETS) markers placed this genus in a clade with Chevreulia, Cuatrecasasiella, Antennaria, and Diaperia in the FLAG group. Affinities of the new genus with genera previously assigned to Chryselium are also discussed.
Data from: The faces of Bacidia schweinitzii: molecular and morphological data reveal three new species including a widespread sorediate morph
Bacidia schweinitzii is a common crustose lichen that is widespread in eastern North America. It is comprised of three distinct morphotypes differing in apothecial pigmentation. Here we show that molecular data from the mtSSU region affirms the distinctiveness of these morphotypes, prompting the recognition of three species: B. schweinitzii s.str., B. ekmaniana sp. nov. and B. purpurans sp. nov. We also show that a common sorediate crustose lichen, sympatric with B. schweinitzii, represents a monophyletic lineage whose relationship with B. schweinitzii s.str. could not be resolved with certainty using analyses of ITS and mtSSU sequence data. We recognize this sorediate lineage as a distinct species, B. sorediata sp. nov. All four taxa are described, illustrated and mapped.
Data from: What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen
Range-expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty-seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analyzing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15°C and more slowly at 28 and 32°C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade-off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.
Data from: A new species of Coryphophylax fitzinger in: Steindachner, 1867 (Sauria: Iguania: Agamidae) from the Andaman Islands, India
The systematic position of the agamid genus Coryphophylax (Squamata: Agamidae) is given as monotypic and endemic to the Andaman and Nicobar Islands in the Bay of Bengal, India. After having surveyed intensively in thirteen different Islands and examined several individuals in the Andamans group of islands, we describe a second species of Coryphophylax from the lowland rainforests of the South Andaman Island. Coryphophylax brevicaudus sp. nov. is differentiated from its congener, C. subcristatus (Blyth, "1860" 1861) by its smaller size, relatively shorter tail, presence of nuchal and dorsal crests in both sexes, midbody scale row counts and colour pattern. The new species lives in sympatry with C. subcristatus. The taxonomic history and systematic status of the genus Coryphophylax are discussed, and the need for continued surveys in the Islands is emphasized.
Data from: Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birds
Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World that comprises ~8% of all bird species, may be the true driver of this rate increase. Understanding the patterns and processes of diversification of this diverse lineage may go a long way toward explaining the apparently rapid diversification rates of both passerines and of birds as a whole. We present the first multi-locus phylogenetic analyses of this endemic New World radiation of finch relatives that includes sampling of all recognized genera, a relaxed molecular clock analysis of its divergence history, and an analysis of its broad-scale diversification patterns. These analyses recover five major lineages traditionally recognized as avian families, but identify an additional ten relatively ancient lineages worthy of recognition at the family level. Time-calibrated diversification analyses suggest that at least six of the fifteen family-level lineages are significantly species-poor given the entire group's background diversification rate, whereas one—the tanagers of family Thraupidae—is significantly more diverse. These differences are consistent with the low speciation and extinction rates of island and ecologically-specialized lineages previously documented across passerines as a whole. Finally, lack of an age-diversity relationship within this clade suggests that, due to rapid initial speciation, it may have experienced density-dependent ecological limits on its overall diversity.
Data from: Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea
The family Melanotaeniidae (rainbowfishes) represents the largest monophyletic group of freshwater fishes found in Australia and New Guinea. The family consists of seven genera and a total of 81 species, which are broadly distributed throughout the region. We conducted a phylogenetic analysis of Melanotaeniidae based on nearly complete taxonomic sampling of all species. We sequenced seven protein coding mitochondrial genes and the first two introns of the nuclear S7 gene, for a total of 6827 base pairs. Our goal was to use the phylogeny to infer the biogeographic history of rainbowfishes in this region, to provide a framework for the timing of divergence within the family, and to test for possible introgression between species. We found strong support for the monophyly of Melanotaeniidae. Three species-poor genera-Cairnsichthys, Rhadinocentrus and Iriatherina-were all resolved as early branching lineages within the family. The three species-rich genera-Melanotaenia, Chilatherina and Glossolepis-did not form a single monophyletic group, but instead formed three monophyletic groups endemic to discrete geographic regions: western New Guinea, northern New Guinea, and southern New Guinea plus Australia, respectively. All three geographic regions also contained three to four additional lineages that were separated by large genetic divergences and were frequently sympatric (except in western New Guinea). Our molecular clock results provide much older estimates of divergence than some aspects of the present geological setting. For instance, the formation of the present day Central Highlands, the integration of the Birds Head region with the rest of New Guinea, and the present proximate position of Waigeo and Batanta islands relative to the Birds Head, are all younger than the rainbowfishes living there based on our molecular clock estimates. We also identified ten species that have likely experienced historical introgression. Most introgression events were between different groups within the northern New Guinea lineage and the Southern New Guinea/Australian lineages. Finally, we identified nearly 20 undescribed species within Melanotaeniidae, demonstrating that much work remains in describing freshwater fish diversity in this region.
Data from: Multilocus phylogenetics of new world milkweed vines (Apocynaceae, Asclepiadoideae, Gonolobinae)
Subtribe Gonolobinae of the cosmopolitan family Apocynaceae is diverse and represents the largest radiation of milkweeds in the New World (~500 species). The largest genus, Matelea, is an amalgam that was united largely by a perceived lack of discrete morphological variation, particularly in floral structures. Using plastid and nuclear DNA sequences, we estimate a phylogeny of Gonolobinae using four chloroplast loci and three cloned nuclear regions. We investigate monophyly of Matelea and other established and provisional genera via a series of hypothesis tests. We find variable support and considerable conflict among the gene trees. Despite this, our data confirm the paraphyly of Matelea while Gonolobus and other segregate genera receive some support as monophyletic assemblages. We attribute conflicting signal in our data primarily to incomplete lineage sorting, a likely result of rapid radiation. Ancestral character reconstructions of growth form, fruit, and corolla morphology reveal a woody twining growth form to be plesiomorphic with one to two transitions to an herbaceous, non-twining growth form followed by one putative reversal to the woody twining growth form in the subtribe. Plesiomorphic states for fruit ornamentation and corolla shape are less clear and these characters exhibit high levels of homoplasy. This study is one of the most comprehensive phylogenies of gonoloboid milkweeds to date and the first to sample multiple nuclear loci and include allelic data.
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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.