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Data from: Small N e of the isolated and unmanaged horse population on Sable Island
For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes. Here, we estimated the effective population size (N e) of the Sable Island horses to assess the risk to this population of these genetic threats. We found surprising consistency of N e estimates across the 5 different methods used, with a mean of 48 effective individuals. This estimate falls below the 50 criterion of the "50/500 rule," below which inbreeding depression is a concern for population viability. However, simulations and knowledge of population history indicate that this population is still in its early stages of approaching equilibrium between mutation, drift, and genetic diversity; and no negative consequences have been identified that could be associated with inbreeding depression. Therefore, we do not recommend taking management action (such as translocations) at this stage. Rather, we propose continued monitoring of genetic diversity and fitness over time so that trends and any substantial changes can be detected. This represents one of the few unmanaged horse populations in the world, and therefore these data will not only alert us to serious concerns regarding their conservation status, but will also provide a wealth of information about how natural processes drive patterns of reproduction, mortality, and population growth over time.
Data from: Current climate, isolation and history drive global patterns of tree phylogenetic endemism
Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions, and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants, and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g. mean annual temperature), geographical characteristics (e.g. isolation) and historical conditions (e.g. tree cover at the last glacial maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the last glacial maximum was a positive predictor of PE in the Paleotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographic, historical, and current factors. Some geographic variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographic drivers and regional climatic histories.
Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis
Background: Mycoplasma bovis is an important pathogen causing pneumonia, mastitis and arthritis in cattle worldwide. As this agent is primarily transmitted by direct contact and spread through animal movements, efficient genotyping systems are essential for the monitoring of the disease and for epidemiological investigations. The aim of this study was to compare and evaluate the multi locus sequence typing (MLST) and the multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) through the genetic characterization of M. bovis isolates from Hungary. Results: Thirty one Hungarian M. bovis isolates grouped into two clades by MLST. Two strains had the same sequence type (ST) as reference strain PG45, while the other twenty nine Hungarian isolates formed a novel clade comprising five subclades. Isolates originating from the same herds had the same STs except for one case. The same isolates formed two main clades and several subclades and branches by MLVA. One clade contained the reference strain PG45 and three isolates, while the other main clade comprised the rest of the strains. Within-herd strain divergence was also detected by MLVA. Little congruence was found between the results of the two typing systems. Conclusions: MLST is generally considered an intermediate scale typing method and it was found to be discriminatory among the Hungarian M. bovis isolates. MLVA proved to be an appropriate fine scale typing tool for M. bovis as this method was able to distinguish closely related strains isolated from the same farm. We recommend the combined use of the two methods for the genotyping of M. bovis isolates. Strains have to be characterized first by MLST followed by the fine scale typing of identical STs with MLVA.
Data from: Model-based species delimitation: are coalescent species reproductively isolated?
A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.
Data from: Oviposition traits generate extrinsic postzygotic isolation between two pine sawfly species
Background: Although empirical data indicate that ecological speciation is prevalent in nature, the relative importance of different forms of reproductive isolation and the traits generating reproductive isolation remain unclear. To address these questions, we examined a pair of ecologically divergent pine-sawfly species: while Neodiprion pinetum specializes on a thin-needled pine (Pinus strobus), N. lecontei utilizes thicker-needled pines. We hypothesized that extrinsic postzygotic isolation is generated by oviposition traits. To test this hypothesis, we assayed ovipositor morphology, oviposition behavior, and host-dependent oviposition success in both species and in F1 and backcross females. Results: Compared to N. lecontei, N. pinetum females preferred P. strobus more strongly, had smaller ovipositors, and laid fewer eggs per needle. Additionally, we observed host- and trait-dependent reductions in oviposition success in F1 and backcross females. Hybrid females that had pinetum-like host preference (P. strobus) and lecontei-like oviposition traits (morphology and egg pattern) fared especially poorly. Conclusions: Together, these data indicate that maladaptive combinations of oviposition traits in hybrids contribute to extrinsic postzygotic isolation between N. lecontei and N. pinetum, suggesting that oviposition traits may be an important driver of divergence in phytophagous insects.
Data from: Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation
A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history, and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions, and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction-site associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.
FIGURE 1 in Anteaglonium saxicola (Anteagloniaceae, Pleosporales), a new species isolated from rocks in northern Thailand
FIGURE 1. Phylogram derived from maximum likelihood analysis of a combined nrLSU, nrSSU, ITS, and tef1-α genes of 26 sequences. Bootstrap values ≥ 75% ML (left) and Bayesian posterior probabilities ≥ 0.90 (right) are shown above nodes. The scale bar represents the expected number of nucleotide substitutions per site. Sequence data obtained from this study are in red. Ex-type strains are in bold.
FIGURE 2 in Anteaglonium saxicola (Anteagloniaceae, Pleosporales), a new species isolated from rocks in northern Thailand
FIGURE 2. Anteaglonium saxicola (SDBR-CMU481, ex-type). Colonies incubated at 25°C for four weeks. a. PDA. b. MEA. c. CMD (left, surface view and right, reverse view). d, e. Conidiomata forming on PDA after incubation at 25°C for two months. f. Vertical section of conidiomata. g. Conidiomata wall. h. Conidiogenous cells. i. Conidia. Scale bars: a–c = 10 mm, d = 500 µm, e, f = 100 µm, g–i = 10 µm.
Host-associated bacteria isolated from animals with chemosynthetic symbionts
<p>Phylogenetic affiliation of bacteria isolated from homogenates of gutless oligochaete worms (<em>Olavius</em> spp.) and from gill tissue of lucinid clams (<em>Loripes lucinalis</em>) and bathymodiolin mussles (<em>Bathymodiolus brooksi</em>).</p>
FIGURES 9–11 in A new species of freshwater crab of the genus Microthelphusa (Brachyura: Pseudothelphusidae) from a remote isolated cloud forest on a tabletop mountain in western Guyana, South America
FIGURES 9–11. Microthelphusa meansi new species. Male holotype, cw 22.5 mm, from the Wokomung Massif, Guyana, USNM 1098373, left first gonopod. 9, caudal view; 10, lateral view; 11, cephalic view. Scale = 3.0 mm.
FIGURES 1–8 in A new species of freshwater crab of the genus Microthelphusa (Brachyura: Pseudothelphusidae) from a remote isolated cloud forest on a tabletop mountain in western Guyana, South America
FIGURES 1–8. Microthelphusa meansi new species. Male holotype, cw 22.5 mm, from the Wokomung Massif, Guyana, USNM 1098372. 1, carapace, dorsal view; 2, cephalothorax, frontal view; 3, right cheliped, frontal view; 4, left cheliped, frontal view; 5, carpus and merus of right cheliped, dorsal view; 6, carpus and merus of right cheliped, inferior view; 7, left third maxilliped; 8, sternum. Scale = 3.2 mm (1, 2), 3.5 mm (3–8).
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 in First record of Hexaglandula corynosoma (Travassos, 1915) Petrochenko, 1958 (Acanthocephala: Polymorphidae) in intermediate and definitive hosts in Mexico
FIGURE 4. Maximum parsimony cladogram depicting phylogenetic relationships among 11 isolates representing 4 species of polymorphids. Numbers in internodes represent bootstrap support values for the Neighbor-Joining and Parsimony analyses, respectively. * = Cystacanth of Hexaglandula corynosoma.
FIGURE 22 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURE 22. Distribution of P. michaelseni (dots) P. baylyi sp. n. (diamonds) and P. ursulae sp. n. (star). The map was made by using MS ENCARTA 2000.
FIGURES 2–7 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 2–7. Habitus of 2) Paroster baylyi sp. n. (male); 3) P. baylyi sp. n. (female); 4) P. u r s u l a e sp. n. (male); 5) P. ursulae sp. n. (female); 6) P. michaelseni (holotype, male); 7) P. michaelseni (female).
FIGURES 8–19 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 8–19. Median lobe of aedeagus in ventral and lateral view: 8) Paroster michaelseni (holotype), 9) P. baylyi sp. n., 10) P. u r s u l a e sp. n.; Left paramere: 11) P. michaelseni (holotype), 12) P. baylyi sp. n., 13) P. u r s u l a e sp. n.; Gonocoxae: 14) P. michaelseni, 15) P. baylyi sp. n., 16) P. u r s u l a e sp. n.; Gonocoxosternum: 17) P. michaelseni, 18) P. baylyi sp. n., 19) P. u r s u l a e sp. n.
FIGURES 23–28 in Paroster baylyi sp. n., P. ursulae sp. n. (Col. Dytiscidae, Hydroporinae) and the water beetle diversity of pan-gnammas on isolated granite outcrops in the Mallee of south-western Australia
FIGURES 23–28. Habitats of Paroster baylyi sp. n. and P. ursulae sp. n., various pan-gnammas: 23) Type locality of P. ursulae sp. n., granite outcrop 80 km WSW Coolgardie {10}; 24) Stephan Gottwald searching for P. ursulae sp. n. {10}; 25) Type localities of P. baylyi sp. n., "Bilya Rock", 25 km ENE Morawa {1}; 26, 27) "Camel Soak", 31 km E Perenjori {2}; 28) "Rockpools", 10 km E Wubin {3}.
FIGURE 1. Aphelenchoides paradalianensis n in Aphelenchoides paradalianensis n. sp. (Nematoda: Aphelenchoididae) isolated at Guangzhou, China, in packaging wood from South Korea
FIGURE 1. Aphelenchoides paradalianensis n. sp. A: Entire female; B: Entire male; C: Female anterior region; D: Vulval region; E: Lateral field; F: Female tail; G–H: Female tail termini; I: Lateral view of male tail; J: Male tail terminus; K: Ventral view of male tail. (All scale bars are 20 µm)
FIGURE 3 in Aphelenchoides paradalianensis n. sp. (Nematoda: Aphelenchoididae) isolated at Guangzhou, China, in packaging wood from South Korea
FIGURE 3. Scanning Electron Microscopy (SEM) observation of Aphelenchoides paradalianensis n. sp. A: Female head; B: Lateral field;. C: Female tail; D–F: Female tail tip.
FIGURE 2. Aphelenchoides paradalianensis n in Aphelenchoides paradalianensis n. sp. (Nematoda: Aphelenchoididae) isolated at Guangzhou, China, in packaging wood from South Korea
FIGURE 2. Aphelenchoides paradalianensis n. sp. A: Entire female; B: Entire male; C: Female anterior region; D: Vulval region; E: Genital tract of female; F: Genital tract of male; G–I: Female tail; J–O: male tail. (All scale bars are 20 µm).
FIGURE 1 in Description of a new shrew of the genus Cryptotis (Mammalia: Soricomorpha: Soricidae) from the Sierra de Aroa, an isolated mountain range in northwestern Venezuela, with remarks on biogeography and conservation
FIGURE 1. External appearance of Cryptotis aroensis. A, lateral view of the holotype (CVULA I–8548), which had a headand-body length of 81mm, and a tail length of 40 mm (Table 1); B, ventral view of the holotype; C, ventral view of the right hindfoot of a paratype (CVULA I–8546), which had a length of 13 mm (Table 1). Photographs by J. Molinari.
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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.