Chromosome-level genome assembly of the yellow boxfish (Ostracion cubicus) provides insights into the evolution of bone plates and ostracitoxin secretion

The Ostracion cubicus, commonly known as the yellow boxfish, is a remarkable species with a body encased in a bone plate and the ability to produce an ostracitoxin from their skin when under stress. However, the genetic basis of those effective defense traits is still largely unknown due to the lack of genomic resources. Here, we assembled the first chromosome-level genome of O. cubicus with 867.50 Mb in genome size and 34.86 Mb N50 scaffold length by HiFi and Hi-C sequencing. Twenty-five pseudo-chromosomes, numbered according to size, covered 94.13% of the total assembled sequences. A total of 23,224 protein-coding genes were predicted, with a BUSCO completeness of 98.6%. Positive selection or rapid evolution was observed in genes related to scale and bone development (acsl4a, casr, keap1a, tbx1), and up-regulation of transcription was found in the skin of boxfish (bmp1, bmp2k, bmp4, bmp7, smad5, suco, prelp, mitf), likely associated with the bone plates evolution in the yellow boxfish. An expansion of the solute carrier family 22, a cluster of genes in solute carrier (SLCs) family, transmembrane protein family (TMEMs), vesicle trafficking (SECs), ATP-binding cassette (ABCs) and apolipoproteins (APOs) were identified under positive selection, rapid evolution, or up-regulated in the skin of boxfish, likely associated with the ostracitoxin secretion in the yellow boxfish. Our study not only presents a high-quality boxfish genome but also provides insights into bone plates evolution and ostracitoxin secretion of O. cubicus

Choice of analytical method can have dramatic effects on primate home range estimates

Primate home range sizes can vary tremendously as a consequence of the analytical technique chosen to estimate home range. This is exemplified by a recent dataset on free ranging snub-nosed monkeys (Rhinopithecus bieti) in Northwest Yunnan, China. Our findings show that the grid cell method cannot substitute for the minimum convex polygon (MCP) method and vice versa. MCP-based estimates are far too large, especially when the form of the home range is irregular due to forays into peripheral areas. Here, we propose an adjusted polygon method, whereby unsuitable and never visited areas are clipped out from the polygon, thus producing more accurate results. Compared to the grid cell method, the adjusted MCP is much more robust when the number of group relocations is limited; MCP turned out to be the method of choice for calculation of monthly and seasonal home ranges. The grid cell method on the other hand yielded the most precise estimates for total or annual home ranges. The style of ranging exhibited by a given primate taxon or population determines which analytical procedures should be applied to estimate home range size, and we would stress the need for thorough evaluation of the pros and cons of home range estimators before conducting field work and analysing dat

Dietary Profile of Rhinopithecus bieti and Its Socioecological Implications

To enhance our understanding of dietary adaptations and socioecological correlates in colobines, we conducted a 20-mo study of a wild group of Rhinopithecus bieti (Yunnan snub-nosed monkeys) in the montane Samage Forest. This forest supports a patchwork of evergreen broadleaved, evergreen coniferous, and mixed deciduous broadleaved/coniferous forest assemblages with a total of 80 tree species in 23 families. The most common plant families by basal area are the predominantly evergreen Pinaceae and Fagaceae, comprising 69% of the total tree biomass. Previous work has shown that lichens formed a consistent component in the monkeys' diet year-round (67%), seasonally complemented with fruits and young leaves. Our study showed that although the majority of the diet was provided by 6 plant genera (Acanthopanax, Sorbus, Acer, Fargesia, Pterocarya, and Cornus), the monkeys fed on 94 plant species and on 150 specific food items. The subjects expressed high selectivity for uncommon angiosperm tree species. The average number of plant species used per month was 16. Dietary diversity varied seasonally, being lowest during the winter and rising dramatically in the spring. The monkeys consumed bamboo shoots in the summer and bamboo leaves throughout the year. The monkeys also foraged on terrestrial herbs and mushrooms, dug up tubers, and consumed the flesh of a mammal (flying squirrel). We also provide a preliminary evaluation of feeding competition in Rhinopithecus bieti and find that the high selectivity for uncommon seasonal plant food items distributed in clumped patches might create the potential for food competition. The finding is corroborated by observations that the subjects occasionally depleted leafy food patches and stayed at a greater distance from neighboring conspecifics while feeding than while resting. Key findings of this work are that Yunnan snub-nosed monkeys have a much more species-rich plant diet than was previously believed and are probably subject to moderate feeding competitio

Landscape features influence gene flow as measured by cost-distance and genetic analyses: a case study for giant pandas in the Daxiangling and Xiaoxiangling Mountains

<p>Abstract</p> <p>Background</p> <p>Gene flow maintains genetic diversity within a species and is influenced by individual behavior and the geographical features of the species' habitat. Here, we have characterized the geographical distribution of genetic patterns in giant pandas (<it>Ailuropoda melanoleuca</it>) living in four isolated patches of the Xiaoxiangling and Daxiangling Mountains. Three geographic distance definitions were used with the "isolation by distance theory": Euclidean distance (EUD), least-cost path distance (LCD) defined by food resources, and LCD defined by habitat suitability.</p> <p>Results</p> <p>A total of 136 genotypes were obtained from 192 fecal samples and one blood sample, corresponding to 53 unique genotypes. Geographical maps plotted at high resolution using smaller neighborhood radius definitions produced large cost distances, because smaller radii include a finer level of detail in considering each pixel. Mantel tests showed that most correlation indices, particularly bamboo resources defined for different sizes of raster cell, were slightly larger than the correlations calculated for the Euclidean distance, with the exception of Patch C. We found that natural barriers might have decreased gene flow between the Xiaoxiangling and Daxiangling regions.</p> <p>Conclusions</p> <p>Landscape features were found to partially influence gene flow in the giant panda population. This result is closely linked to the biological character and behavior of giant pandas because, as bamboo feeders, individuals spend most of their lives eating bamboo or moving within the bamboo forest. Landscape-based genetic analysis suggests that gene flow will be enhanced if the connectivity between currently fragmented bamboo forests is increased.</p

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences

<p>Abstract</p> <p>Background</p> <p>The Salangid icefish <it>Neosalanx taihuensis </it>(Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.</p> <p>Results</p> <p>We obtained the complete mtDNA cytochrome <it>b </it>sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).</p> <p>Conclusion</p> <p>The observed complex genetic pattern of <it>N. taihuensis </it>is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.</p

A single nucleotide mutation in the dual-oxidase 2 (DUOX2) gene causes some of the panda's unique metabolic phenotypes

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13030100 and XDB29020000), the Creative Research Group Project of National Natural Science Foundation of China (31821001), the Key Project of the Chinese Academy of Sciences (QYZDB-SSW-SMC047), the National Key Research and Development Program of China (2018YFC2000500), the Chinese Academy of Sciences President's International Fellowship Initiative Postdoctoral Fellowship (to A.M.R.) and the President's International Fellowship Initiative Professorial and Wolfson Merit Award (to J.R.S.).Peer reviewedPublisher PD

Single-Junction Binary-Blend Nonfullerene Polymer Solar Cells with 12.1% Efficiency

A new fluorinated nonfullerene acceptor, ITIC-Th1, has been designed and synthesized by introducing fluorine (F) atoms onto the end-capping group 1,1-dicyanomethylene-3-indanone (IC). On the one hand, incorporation of F would improve intramolecular interaction, enhance the push–pull effect between the donor unit indacenodithieno[3,2-b]thiophene and the acceptor unit IC due to electron-withdrawing effect of F, and finally adjust energy levels and reduce bandgap, which is beneficial to light harvesting and enhancing short-circuit current density (JSC). On the other hand, incorporation of F would improve intermolecular interactions through C-F···S, C-F···H, and C-F···π noncovalent interactions and enhance electron mobility, which is beneficial to enhancing JSC and fill factor. Indeed, the results show that fluorinated ITIC-Th1 exhibits redshifted absorption, smaller optical bandgap, and higher electron mobility than the nonfluorinated ITIC-Th. Furthermore, nonfullerene organic solar cells (OSCs) based on fluorinated ITIC-Th1 electron acceptor and a wide-bandgap polymer donor FTAZ based on benzodithiophene and benzotriazole exhibit power conversion efficiency (PCE) as high as 12.1%, significantly higher than that of nonfluorinated ITIC-Th (8.88%). The PCE of 12.1% is the highest in fullerene and nonfullerene-based single-junction binary-blend OSCs. Moreover, the OSCs based on FTAZ:ITIC-Th1 show much better efficiency and better stability than the control devices based on FTAZ:PC71BM (PCE = 5.22%)

Karriere-Handbuch

We design and synthesize four fused-ring electron acceptors based on 6,6,12,12-tetrakis(4-hexylphenyl)- indacenobis(dithieno[3,2-b;2′,3′-d]thiophene) as the electron- rich unit and 1,1-dicyanomethylene-3-indanones with 0− 2 fluorine substituents as the electron-deficient units. These four molecules exhibit broad (550−850 nm) and strong absorption with high extinction coefficients of (2.1−2.5) × 105 M−1 cm−1. Fluorine substitution downshifts the LUMO energy level, red-shifts the absorption spectrum, and enhances electron mobility. The polymer solar cells based on the fluorinated electron acceptors exhibit power conversion efficiencies as high as 11.5%, much higher than that of their nonfluorinated counterpart (7.7%). We investigate the effects of the fluorine atom number and position on electronic properties, charge transport, film morphology, and photovoltaic properties

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level