Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto).

As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.

Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea.

Bats are reservoir hosts of many zoonotic viruses with pandemic potential. We utilized single-cell transcriptome sequencing (scRNA-seq) to analyze the immune response in bat lungs upon in vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Bat neutrophils were distinguished by high basal IDO1 expression. NK cells and T cells were the most abundant immune cells in lung tissue. Three distinct CD8+ effector T cell populations could be delineated by differential expression of KLRB1, GFRA2, and DPP4. Select NK and T clusters increased expression of genes involved in T cell activation and effector function early after viral infection. Alveolar macrophages and classical monocytes drove antiviral interferon signaling. Infection expanded a CSF1R+ population expressing collagen-like genes, which became the predominant myeloid cell type post-infection. This work uncovers features relevant to viral disease tolerance in bats, lays a foundation for future experimental work, and serves as a resource for comparative immunology studies.

Transgenic Maize Has Insignificant Effects on the Diversity of Arthropods: A 3-Year Study.

In order to provide more evidence for the evaluation of the ecological risks of transgenic maize, arthropod population dynamics and biodiversity in fields planted with two kinds of transgenic maize (DBN9868, expressing the PAT and EPSPS genes, and DBN9936, expressing the Cry1Ab and EPSPS gene) were investigated by direct observation and trapping for three years. The recorded arthropod species belonged to 19 orders and 87 families, including Aphidoidea, Chrysomelidae, Coccinellidae, Chrysopidae and Araneae. The species richness, Shannon-Wiener diversity index, Pielou evenness index, dominance index and community similarity index of arthropod communities in maize fields were statistically analyzed, and the results showed that (1) the biodiversity difference of arthropod communities between transgenic maize and non-transgenic maize was smaller than that between different conventional cultivars; (2) the differences between ground-dwelling arthropod communities were less obvious than those between plant-inhabiting arthropod communities; and (3) Lepidoptera, the target pests of Bt maize, were not the dominant population in maize fields, and the dominant arthropod population in maize fields varied greatly between years and months. Combining those results, we concluded that the transgenic maize DBN9868 and DBN9936 had no significant effect on the arthropod communities in the field.

Microbiome diversity of cotton aphids (Aphis gossypii) is associated with host alternation.

Aphids are infected by a series of bacteria that can help them survive on specific host plants. However, the associations between aphids and these bacteria are not clear, and the bacterial communities in many aphid species are poorly characterized. Here, we investigated the bacterial communities of cotton aphids (Aphis gossypii) on 2 representative winter host plants and transferred to 3 summer host plants by 16S rDNA sequencing using the Illumina MiSeq platform. Our results revealed that the bacterial communities varied among cotton aphids on hibiscus, cotton aphids on pomegranate, cotton aphids on cotton transferred from hibiscus, cotton aphids on muskmelon transferred from hibiscus, cotton aphids on cucumber transferred from hibiscus,. The diversity and richness of the bacterial communities were significantly higher in aphids on muskmelon and aphids on cucumber than in the other treatments. There were two main factors influencing the distribution of internal bacterial OTUs revealed by principal component analysis, including the differences among Punicaceae, Malvaceae and Cucurbitaceae. There were 28 bacterial communities with significant differences between two arbitrary treatments, which could be grouped into 6 main clusters depending on relative abundance. Moreover, our results indicated that in addition to the obligate endosymbiont Buchnera, with a dominant position (> 52%), A. gossypii also harbored 3 facultative endosymbiotic bacteria (Serratia, Arsenophonus, and Wolbachia) and 3 possibly symbiotic bacteria (Acinetobacter, Pantoea, and Flavobacterium). There were several correspondences between the symbiotic bacteria in cotton aphids and the specific host plants of the aphids. This study provides a better understanding of the interactions among symbiotic bacteria, aphids and host plants, suggesting that the selection pressure on aphid bacterial communities is likely to be exerted by the species of host plants.