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Molecular Formulas of Organic Aerosols at Two Sites of East China
<p>In this dataset we present molecular composition of organic aerosols collected at Xiangshan gulf (29°29′ N, 121°46′ E) and an inland urban site (32°20′ N, 118°71′ E) of east China. Compound formula, mass-to-charge ratio, mass error between measured and theoritical values, intensity and adduct form are measured using a FT-ICR-MS with a high size resolution.</p>
Figure 10 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 10. Plate showing the cranium and mandible of Pseudoromicia nyanza (FMNH 215626). Scale bar = 5 mm.
Figure 9 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 9. Plate showing the cranium and mandible of Pseudoromicia kityoi (FMNH 223211). Scale bar = 5 mm.
Figure 8. A in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 8. A, portrait of Laephotis kirinyaga (FMNH 234558), showing bright brown upper parts and off-white under parts, with bicoloured hairs. The skin around the eye is blackish in the holotype, but distinctly pinkish in most of the paratypes. B, portrait of Pseudoromicia nyanza (FMNH 215626), showing the distinctive white wings and under parts of this species.
Figure 7 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 7. Plate showing the cranium and mandible of Laephotis kirinyaga (FMNH 234558). Scale bar = 5 mm.
Figure 5 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 5. Bacula of the four clades within formerly or traditionally recognized as Neoromicia: A, Laephotis kirinyaga (FMNH 234639); B, Neoromicia somalica (FMNH 215614); C, Pseudoromicia kityoi (FMNH 223211); and D, Afronycteris nana (DM 13013). Note the three-pronged tip in Neoromicia, the straight shaft with spatulate tip at an angle of 45° in Laephotis, the long, curved shaft with bilobed tip in Pseudoromicia and the deeply bilobed base and gently curved shaft in Afronycteris. Scale bars: 1 mm.
Figure 2 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 2. Maximum likelihood phylogeny of intergeneric relationships of mitochondrial cytochrome b sequences of Vespertilionidae. The phylogeny was inferred in IQ-TREE, and its topology was similar to the Bayesian phylogeny calculated in MRBAYES. Bootstrap (BS) values followed by Bayesian posterior probabilities (PP) are indicated adjacent to nodes (those nodes with both BS <70% and PP <0.95 are not labelled).
Figure 6 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 6. Principal components analysis of craniodental characters of the short-eared species of Laephotis as recognized in this study.
Figure 4 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 4. Principal components analysis of craniodental measurements of the species traditionally allocated to the genus Neoromicia s.l.; the colours correspond to the four distinct types of bacula exhibited by these species (shown in Fig. 5). Each dot refers to the mean value of the craniodental measurements of examined specimens; see main text for further details.
Figure 3 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 3. Maximum likelihood phylogeny of mitochondrial cytochrome b sequences of Vespertilionidae: (A) Pipistrellus, Scotoecus, Vansonia, and outgroups (B) Afronycteris, Pseudoromicia, Nycticeinops, and Hypsugo (C) Laephotis and Neoromicia. The phylogeny was inferred in IQ-TREE, and its topology was similar to the Bayesian phylogeny calculated in MRBAYES. Filled red circles on nodes denote bootstrap (BS) values ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95. Open circles outlined in black indicate BS ≥ 70% and PP <0.95, and open circles outlined in red indicate BS <70% and PP> 0.95. Support values for most minor clades are not shown. Specimen localities include counties for Kenya. DRC refers to Democratic Republic of the Congo and CAR to Central African Republic. Museum acronyms are defined in the Material and Methods section. Sequences downloaded from GenBank are indicated by inclusion of GenBank accession numbers (Supporting Information, Table S1). Branch colours indicate individual species/clade membership.
Figure 1 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species
Figure 1. Type localities of taxa of African and Malagasy Vespertilionini and Pipistrellini. Valid species are denoted by filled circles, subspecies and synonyms by open circles and species described herein by stars: 1, Pipistrellus abaensis J. A. Allen, 1917; 2, N[ycticejus]. adovanus Heuglin, 1877; 3, Pipistrellus aero Heller, 1912; 4, Vespertilio pipistrellus var. africanus Rüppell, 1842; 5, Nycticeius africanus G. M. Allen, 1911; 6, Scotoecus albigula Thomas, 1909; 7, Scoteinus schlieffeni albiventer Thomas & Wroughton, 1908; 8, Scotophilus albofuscus Thomas, 1890; 9, Vesperugo anchietae Seabra, 1900; 10, Laephotis angolensis Monard, 1935; 11, Eptesicus capensis angolensis Hill, 1937; 12, Pipistrellus ariel Thomas, 1904; 13, Scotoecus artinii De Beaux, 1923; 14, Eptesicus ater J. A. Allen, 1917; 15, Pipistrellus nanus australis Roberts, 1913; 16, Scoteinus schlieffeni australis Thomas & Wroughton, 1908; 17, Scoteinus schlieffeni bedouin Thomas & Wroughton, 1908; 18, Pipistrellus eisentrauti bellieri De Vree, 1972; 19, Hypsugo bemainty Goodman et al., 2015; 20, Vesperus bicolor Bocage, 1889; 21, Laephotis botswanae Setzer, 1971; 22, Pipistrellus (Romicia) kuhlii broomi Roberts, 1948; 23, Vesperugo (Vesperus) brunneus Thomas, 1880; 24, Vespertilio capensis A. Smith, 1829; 25, Scotoecus cinnamomeus Wettstein, 1916; 26, Pipistrellus crassulus Thomas, 1904; 27, Pipistrellus culex Thomas, 1911; 28, Vesperus damarensis Noack, 1889; 29, Scotophilus darwini Tomes, 1859; 30, Pipistrellus deserti Thomas, 1902; 31, Pipistrellus eisentrauti Hill, 1968; 32, Scotoecus falabae Thomas, 1915; 33, Eptesicus faradjius J. A. Allen, 1917; 34, Scoteinus schlieffeni fitzsimonsi Roberts, 1932; 35, Pipistrellus fouriei Thomas, 1926; 36, Pipistrellus kuhlii fuscatus Thomas, 1901; 37, Pipistrellus fuscipes Thomas, 1913; 38, Eptesicus garambae J. A. Allen, 1917; 39, Vespertilio capensis gracilior Thomas & Schwann, 1905; 40, Vesperugo (Vesperus) grandidieri Dobson, 1876; 41, Vesperus guineensis Bocage, 1889; 42, Pipistrellus hanaki Hulva & Benda, 2004; 43, Parahypsugo happoldorum Hutterer, Decher, Monadjem & Astrin, 2019; 44, Pipistrellus helios Heller, 1912; 45, Vespertilio hesperida Temminck, 1840; 46, Scotoecus hindei Thomas, 1901; 47, Scotophilus hirundo de Winton, 1899; 48, Vesperus humbloti Milne-Edwards, 1881; 49, Vesperugo hypoleucus Heuglin [in Fitzinger & Heuglin], 1866; 50, Pipistrellus inexspectatus Aellen, 1959; 51, Neoromicia isabella Decher, Hutterer & Monadjem, 2016; 52, Laephotis kirinyaga Monadjem et al., this paper; 53, Pseudoromicia kityoi Monadjem et al., this paper; 54, Hypsugo lanzai Benda, Al-Jumaily, Reiter & Nasher, 2011; 55, Pipistrellus leucomelas Monard, 1932; 56, Parahypsugo macrocephalus Hutterer & Kerbis Peterhans, 2019; 57, Vesperugo maderensis Dobson, 1878; 58, Eptesicus somalicus malagasyensis Peterson, Eger & Mitchell, 1995; 59, Vespertilio marginatus Cretzschmar, 1830; 60, Pipistrellus marrensis Thomas & Hinton, 1923; 61, Vespertilio matroka Thomas & Schwann, 1905; 62, Pipistrellus africanus meesteri Kock, 2001; 63, Eptesicus melckorum Roberts, 1919; 64, Scotophilus minimus Noack, 1887; 65, Pipistrellus minusculus Miller, 1900; 66, Vespertilio minuta Temminck, 1840; 67, Pipistrella minuta Loche, 1867; 68, Pipistrellus musciculus Thomas, 1913; 69, Laephotis namibensis Setzer, 1971; 70, Pipistrellus nanulus Thomas, 1904; 71, Vespertilio nanus Peters, 1852; 72, Eptesicus capensis nkatiensis Roberts, 1932; 73, Scabrifer notius G. M. Allen, 1908; 74, Pseudoromicia nyanza Monadjem et al., this paper; 75, †Scotoecus olduvensis Gunnell, Butler, Greenwood & Simmons, 2015; 76, Vesperugo pagenstecheri Noack, 1889; 77, Pipistrellus (Pipistrellus) permixtus Aellen, 1957; 78, Eptesicus phasma G. M. Allen, 1911; 79, Vespertilio pipistrellus Schreber, 1774; 80, Vespertilio platycephalus Temminck, 1832; 81, Vesperugo pulcher Dobson, 1875; 82, Vesperugo pusillulus Peters, 1870; 83, Pipistrellus raceyi Bates et al., 2006; 84, Eptesicus rectitragus Wettstein, 1916; 85, Vesperugo (Vesperus) rendalli Thomas, 1889; 86, Neoromicia robertsi Goodman et al., 2012; 87, Neoromicia roseveari Monadjem et al., 2013; 88, V[espertilio]. rueppelii J. Fischer, 1829; 89, Scotophilus rusticus Tomes, 1861; 90, Vespertilio savii Bonaparte, 1837; 91, Nycticejus schlieffenii Peters, 1859; 92, Pipistrellus rueppelli senegalensis Dorst, 1960; 93, †Nycticeinops serengetiensis Gunnell et al., 2015; 94, Pipistrellus simandouensis Monadjem et al., 2020; 95, Vespertilio minutus somalicus Thomas, 1901; 96, Vesperugo stampflii Jentink, 1888; 97, Neoromicia stanleyi Goodman et al., 2017; 98, Vesperus tenuipinnis Peters, 1872; 99, Eptesicus ugandae Hollister, 1916; 100, Neoromicia vansoni Roberts, 1932; 101, Pipistrellus vernayi Roberts, 1932; 102, Laephotis wintoni Thomas, 1901; 103, Scotoecus woodi Thomas, 1917; 104, Eptesicus zuluensis Roberts, 1924. Not mapped: [Pipistrellus Kuhli] latastei Laurent, 1937; Vespertilio pusillus LeConte, 1857; Vesperugo subtilis Sundevall, 1846.
Plant sedimentary ancient DNA data from Far East Russia
<p>Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plants is not well understood due to the limited knowledge about plant assembly rules. Past plant diversity over long time series is rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast <i>trnL</i> gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. <i>Larix</i> invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation coverage was densest. We reveal highest richness during 28–23 ka and a second richness peak during 13–10 ka, with both periods being accompanied by low shrub abundance. During the cold period before 14 ka, rich communities were phylogenetically clustered, suggesting low genetic divergence in the communities despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich communities were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness may overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.</p>
A modeling study of the tripole pattern of East China precipitation over the past 425 ka
<p>These files contain the model outputs from Noresm-L that are used to draw the main parts of Figures in our paper entitled "A modeling study of the tripole pattern of East China precipitation over the past 425 ka".</p>
Description and classification of echolocation clicks of Indian Ocean humpback (Sousa plumbea) and Indo-Pacific bottlenose (Tursiops aduncus) dolphins from Menai Bay, Zanzibar, East Africa
<p>Passive acoustic monitoring (PAM) is a powerful method to study the occurrence, movement and behavior of echolocating odontocetes (toothed whales) in the wild. However, in areas occupied by more than one species, echolocation clicks need to be classified into species. The present study investigated whether the echolocation clicks produced by small, at-risk, resident sympatric populations of Indian Ocean humpback dolphin (Sousa plumbea) and Indo-Pacific bottlenose dolphin (Tursiops aduncus) in Menai Bay, Zanzibar, East Africa, could be classified to allow species specific monitoring. Underwater sounds of S. plumbea and T. aduncus groups were recorded using a SoundTrap 202HF in January and June-August 2015. Eight acoustic parameters, i.e. -10 dB duration, peak, centroid, lower -3 and lower -10 dB frequencies, and -3 dB, -10 dB and root-mean-squared bandwidth, were used to describe and compare the two species' echolocation clicks. Statistical analyses showed that S. plumbea clicks had significantly higher peak, centroid, lower -3 and lower -10 dB frequencies compared to T. aduncus, whereas duration and bandwidth parameters were similar for the two species. Random Forest (RF) classifiers were applied to determine parameters that could be used to classify the two species from echolocation clicks and achieved 28.6% and 90.2% correct species classification rates for S. plumbea and T. aduncus, respectively. <a name="_Hlk32088545">Both species were classified at a higher rate than expected at random, however the identified classifiers would only be useful for T. aduncus monitoring.</a> <a name="_Hlk32088580">The frequency and bandwidth parameters provided most power for species classification.</a> <a name="_Hlk32088592">Further study is necessary to identify useful classifiers for S. plumbea.</a> This study represents a first step in acoustic <a name="_Hlk32088605">description </a>and classification of S. plumbea and T. aduncus in the western Indian Ocean region, with potential application for future acoustic monitoring of species-specific temporal and spatial occurrence in these sympatric species.</p>
FIGURE 3. Lathrobium miaoi. A—male sternite V in New species and new records of the genus Lathrobium Gravenhorst (Coleoptera Staphylinidae: Paederinae) from Zhejiang, East China
FIGURE 3. Lathrobium miaoi. A—male sternite V; B—male sternite VI; C—male sternite VII; D—male tergite VIII; E—male sternite VIII; F—aedeagus in ventral view; G—aedeagus in lateral view; H—aedeagus in dorsal view. Scale bars: 0.5 mm.
FIGURE 2. Lathrobium chengi. A—male sternite V in New species and new records of the genus Lathrobium Gravenhorst (Coleoptera Staphylinidae: Paederinae) from Zhejiang, East China
FIGURE 2. Lathrobium chengi. A—male sternite V; B—male sternite VI; C—male sternite VII; D—male tergite VIII; E—male sternite VIII; F—aedeagus in ventral view; G—aedeagus in lateral view; H—aedeagus in dorsal view. Scale bars: 0.5 mm.
Ecological limits as the driver of bird species richness patterns along the east Himalayan elevational gradient
<p>Variation in species richness across environmental gradients results from a combination of historical non-equilibrium processes (time, speciation, extinction) and present-day differences in environmental carrying capacities (i.e., ecological limits, affected by species interactions and the abundance and diversity of resources). In a study of bird richness along the sub-tropical east Himalayan elevational gradient, we test the prediction that species richness patterns are consistent with ecological limits using data on morphology, phylogeny, elevational distribution, and arthropod resources. Species richness peaks at mid-elevations. Occupied morphological volume is roughly constant from low to mid-elevations, implying more species are packed into the same space at mid-elevations compared with low elevations. However, variance in beak length, and differences in beak length between close relatives decline with elevation, a consequence of the addition of many small insectivores at mid-elevations. These patterns are predicted from resource distributions: arthropod size diversity declines from low to mid elevations, largely because many more small insects are present at mid-elevations. Weak correlations of species mean morphological traits with elevation also match predictions based on resources and habitats. Elevational transects in the tropical Andes, New Guinea and Tanzania similarly show declines in mean arthropod size and mean beak length, and in these cases likely contribute to declining numbers of insectivorous bird species richness along these gradients. The results imply conditions for ecological limits are met, although historical non-equilibrium processes are likely to also contribute to the pattern of species richness.</p>
Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between the dominant model of rs877356 and binary TST status in the combined cohort (OR=0.2671, p=1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant rs2069885 had the most significant association (p=1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and T¬H2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected participants with extensive exposure increases the power to detect associations in complex infectious disease.
Data from: Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic
Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.
Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
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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.