One strategy to protect endangered species, and improve the quality of habitat to meet the needs of both the wildlife and human communities that rely on large protected areas (such as national park), is by zoning its management for multiple uses. We assessed whether multi-use zoning of the Giant Panda National Park (GPNP) could achieve the goal of protecting the panda population and its habitat, while also promoting community development. We integrate panda presence data, human disturbance distribution, and environmental factors to evaluate panda habitat suitability, the effectiveness of zoning designations, and the impact of human disturbance on panda habitat. Our results show that panda habitat suitability has been partially improved, as certain areas of increased in suitability or stabilized (maintained suitability) across the research region between 2001–2003 and 2011–2013, based on the 3rd and 4th national surveys of the giant panda. Most of the optimum and suitable habitat for panda were located in the core protection area of the GPNP. However, the optimum habitat in the general control area is often located at the junction with the core protection area, indicating a particular need to strengthen management in these areas. Meanwhile, the encounter rates of livestock grazing were highest in optimum habitat and unsuitable habitat. As such, particular attention needs to be paid to the pressures on wildlife caused by human disturbances, such as livestock grazing, in the general control area. Our analyses and these findings have important implications for giant panda conservation and GPNP construction.
Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
Mulberry is a kind of important medicinal plant and its leaf is the main food sources of silkworm. Previous studies showed that the content of secondary metabolites in mulberry leaves, particularly for moracin N, was increased after UV-B induction. To uncover the effects on the growth and development in silkworm reared on different mulberry leaves, SWATH-based proteomic technique was used to analyze the protein profiles of midgut in silkworm reared on fresh mulberry leaf (FM), UV-B induced mulberry leaf (UVM), and fresh mulberry leaf spread with moracin N (NM), respectively. Compared to the FM group, a total of 90 and 182 proteins were identified as differentially expressed proteins in UVM and NM groups, respectively. Of note, the abundance of vacuolar ATP synthase protein was increased by 17 times. The abundance of proteins related to silkworm disease resistance such as ATP-binding cassette, programmed cell death 6-interacting protein, and ribosomal protein were also increased. GO category and KEGG pathway analysis showed that amino acid metabolism and propanoate metabolism in silkworm were affected by UVM and NM. These results suggest that UVM and NM could be developed as a potential drug for improving the immune system in silkworm.
Large-scale molecular phylogenetic studies of the avian order Strigiformes have been performed, and numerous mitochondrial genomes have been determined. However, their intergeneric relationships are still controversial, and few comprehensive comparative analyses of mitochondrial genomes have been conducted on Strigiformes. In this study, the mitochondrial genome of Otus lettia was determined and compared with other Strigiformes. The O. lettia mitochondrial genome was 16,951 bp in size. For Strigiformes, atp8 can be used as a suitable molecular marker for population genetic diversity, while cox1 is a candidate barcoding marker for species identification. All protein-coding genes may be under strong purifying selection pressure, and one extra cytosine insertion located in nad3 is common to all owls except Tyto longimembris, T. alba, and Athene noctua. Four different mitochondrial gene arrangement types were found among the Strigiformes mitogenomes, and their evolutionary relationship between each other can be perfectly explained by the tandem duplication and random loss model. The phylogenetic topologies using the mitochondrial genomes showed that target species O. lettia had a closer relationship with O. scops + O. sunia than O. bakkamoena, the genus Glaucidium was paraphyletic, and the Ninox clade was located at the basal position of Strigidae lineage. Our phylogenetic trees also supported the previous recommendations that Sceloglaux albifacies, Ciccaba nigrolineata, and Ketupa flavipes should be transferred to Ninox, Strix, and Bubo, respectively. These findings will be helpful in further unraveling the mitochondrial evolution and phylogeny of Strigiformes.
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