Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird.

Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Molecular phylogenetics and diversity of the Himalayan shrew ( Soriculus nigrescens Gray, 1842) (Eulipotyphla, Soricidae) in Southwest China.

The Himalayan shrew, Soriculus nigrescens Gray, 1842, belongs to the monotypic genus Soriculus, which is distributed mainly in the Himalayan region. Previous authors have studied its classification based on morphological and molecular data. However, no comprehensive study of the diversity and phylogeny of this species has been performed. In this study, we investigated the molecular phylogeny, genetic diversity, and species divergence of S. nigrescens based on one mitochondrial gene and three nuclear genes. A total of 124 samples from 27 sites in Southwest China were analyzed. Our molecular phylogenetic analyses and species divergence reveal non-monophyly of Soriculus, potentially representing two genera and three clades. Populations from Yunnan (Clade YN) represent the subspecies S. n. minors and should recover the full species status. Populations from Himalayas (Clade A) represent the species S. nigrescens, while populations from southeastern Nyenchen Tanglha Mountains and southern Himalayas (Clade B) represent a new cryptic and unnamed species. Species delimitation analyses and deep genetic distance analysis clearly support the species status of these three evolving clades. The putative new genus and cryptic species should be studied and identified in the future using a more extensive sampling combined with a comprehensive morphological and phylogenetic analysis.

Molecular phylogeny and taxonomy of the genus Nectogale (Mammalia: Eulipotyphla: Soricidae).

The elegant water shrew, Nectogale elegans, is one of the small mammal species most adapted to a semi-aquatic lifestyle. The taxonomy of the genus Nectogale has received little attention due to difficulties in specimen collection. In this study, we sequenced one mitochondrial and eight nuclear genes to infer the phylogenetic relationship of Nectogale. Phylogenetic analyses revealed two large clades within Nectogale. One clade represented N. elegans, and the other was regarded as N. sikhimensis. The split between N. elegans and N. sikhimensis dated back to the early Pleistocene (2.15 million years ago [Ma]), which might be relevant to the Qinghai-Tibet Plateau (QTP) uplift. The morphological comparison showed several distinguishing characters within Nectogale: the shape of the mastoids, the first lower unicuspid (a1), and the second upper molar (M2). Overall, the molecular and the morphological evidences supported that the genus Nectogale consists of two valid species: N. elegans and N. sikhimensis.

Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns.

The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.

The complete mitochondrial genome of Plagiopholis styani (Reptilia: Squamata: Colubridae).

In this study, the complete mitochondrial genome of Plagiopholis styani was acquired and described. The mitogenome is a circular molecule of 19,669 base pairs (bp) in length including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two control regions (D-loop), which is similar to other Colubridae snakes. The total base composition of mitochondrial DNA is A 33.0%, C 24.9%, G 12.8%, and T 29.3%. The mitochondrial genome of Plagiopholis styani contributes to revealing the phylogenetic relationships among species of the Colubridae family.

The complete mitochondrial genome of white-tailed mole (Parascaptor leucura).

The white-tailed mole (Parascaptor leucura) belongs to genus Parascaptor, which is a monotypic genus distributed across Southwestern China, Assam (India), Bengal, and Northern Burma, and Laos. In this study, we obtained the complete mitochondrial genome of Parascaptor leucura. The genome is total 16,875 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions, with a base composition of 33.5% A, 26.4% T, 25.7% C, and 14.3% G. The nucleotide sequence data of 13 protein-coding genes of P. leucura and other nine Eulipotyphla species were used to reconstruct a Bayesian phylogenetic tree. The tree shows that P. leucura belongs to subfamily Talpinae and is closely related to Scaptochirus moschatus.

Complete mitochondrial genome and phylogenetic analysis of Schizothorax sinensis (Teleostei: Cypriniformes: Cyprinidae).

This study describes the first sequencing of the complete mitochondrial genome of Schizothorax sinensis, a species of cyprinid snowtrout from the Jialing River and Fujiang River basins in China's Sichuan Province. The total length is 16,571 base pairs. Similar to most Schizothoracinae mitochondrial genomes, there are 37 genes including 13 protein coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. In addition, it contains a control region rich in A-T nucleotides. The overall nucleotide composition is 29.6% for A, 27.1% for C, 17.9% for G and 25.4% for T, and the percentage of GC content is 45.0%. Phylogenetic analysis suggested that Schizothorax sinensis and Schizothorax prenanti clustered together in a clade. This work provides additional molecular information for studying Schizothorax sinensis conservation genetics and evolutionary relationships.

DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts.

Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.

The complete mitochondrial genome of Amphiesma optatum.

In this study, we obtained and described the complete mitochondrial genome sequence of Amphiesma optatum. The total length is 17,259 base pairs. Similar to most Colubridae mitochondrial genomes, there are 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and 2 ribosomal RNA genes (rRNA). In addition, it contains two control regions (D-loop) rich in A-T base. The total base composition of mitochondrial DNA is 34.3% for A, 26.5% for C, 12.8% for G, and 26.4% for T, and the percentage of GC content is 39.3%. These data further reveal the phylogenetic relationship between Amphiesma optatum and other species in the Colubridae family.

The complete mitogenome of Smith's shrew (Chodsigoa smithii).

The Smith's shrew (Chodsigoa smithii) belongs to subfamily Soricinae, which is an endemic shrew to China. In this study, we obtained the complete mitochondrial genome of the C. smithii. This mitogenome is a circular molecule with 17,108 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, one light strand replication origin (OL), one non-coding region, and with a base composition of 32.5% A, 29.3% T, 24.8% C, and 13.4% G. The nucleotide sequence data of 13 protein-coding genes of C. smithii and other 19 Soricomorpha species were used for phylogenetic analyses. Phylogenetic tree shows that Soricinae includes two major phylogenetic lineages. Chodsigoa smithii is located as a basal position in tribe Nectogalini.

The complete mitochondrial genome of Omei Treefrog (Rhacophorus omeimontis).

In this study, the complete mitochondrial genome of Rhacophorus omeimontis was obtained and described. The sequenced mitogenome is total 19,604 base pairs (bp) in length, which contained 13 protein-coding genes (PCGS), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 control regions (D-loop). The overall base composition of the mitochondrial DNA is 32.5% for A, 30.5% for T, 23.3% for C, and 13.7% for G, and the percentage of GC content is 37.0%. The complete mitochondrial genome information of R. omeimontis will contribute to revealing the phylogenetic relationships among species of family Rhacophoridae.

Does foliar nutrient resorption regulate the coupled relationship between nitrogen and phosphorus in plant leaves in response to nitrogen deposition?

Nutrient resorption from senescing leaves is an important process of internal nutrient cycling in plants, but the patterns of nutrient resorption and the coupled relationship between nitrogen (N) and phosphorus (P) in plant leaves as affected by N deposition remain unclear. We analysed the effects of N addition on the nutrient resorption and coupled relationship between N and P in plant leaves under different nutrient-limited conditions based on a global meta-analysis. Globally, the mean N resorption efficiency (NRE) and P resorption efficiency (PRE) under natural conditions were 47.4% and 53.6%, respectively, which were significantly regulated by geographical and climatic factors as well as plant characteristics. Furthermore, N addition significantly decreased the NRE by 13.3% but slightly affected the PRE on a global scale, and N addition rates and latitude directly and negatively affected the effects of N addition on NRE. Specifically, N addition significantly decreased the NRE under all nutrient-limited conditions, while it had negative, positive, and neutral effects on the PRE under N-limited, P-limited, and N and P-co-limited conditions, respectively. Moreover, the relationships between N and P in green and senesced leaves were tightly coupled under different nutrient-limited conditions in natural ecosystems. However, N addition significantly weakened the relationships between N and P concentrations in green leaves but slightly affected the relationship in senesced leaves, which were mainly modulated by the effects of N addition on nutrient resorption efficiency, especially NRE. These results highlight that nutrient-limited conditions determine the response of nutrient resorption to N deposition and emphasize the effect of nutrient resorption regulation on the coupling of N and P responses to N enrichment. The findings are important for understanding plant nutrient use strategies and the mechanisms underlying the stoichiometric coupling of N and P in response to climate change, and can be used in global biogeochemical models.

Simple additive simulation overestimates real influence: altered nitrogen and rainfall modulate the effect of warming on soil carbon fluxes.

Experiments and models have led to a consensus that there is positive feedback between carbon (C) fluxes and climate warming. However, the effect of warming may be altered by regional and global changes in nitrogen (N) and rainfall levels, but the current understanding is limited. Through synthesizing global data on soil C pool, input and loss from experiments simulating N deposition, drought and increased precipitation, we quantified the responses of soil C fluxes and equilibrium to the three single factors and their interactions with warming. We found that warming slightly increased the soil C input and loss by 5% and 9%, respectively, but had no significant effect on the soil C pool. Nitrogen deposition alone increased the soil C input (+20%), but the interaction of warming and N deposition greatly increased the soil C input by 49%. Drought alone decreased the soil C input by 17%, while the interaction of warming and drought decreased the soil C input to a greater extent (-22%). Increased precipitation stimulated the soil C input by 15%, but the interaction of warming and increased precipitation had no significant effect on the soil C input. However, the soil C loss was not significantly affected by any of the interactions, although it was constrained by drought (-18%). These results implied that the positive C fluxes-climate warming feedback was modulated by the changing N and rainfall regimes. Further, we found that the additive effects of [warming × N deposition] and [warming × drought] on the soil C input and of [warming × increased precipitation] on the soil C loss were greater than their interactions, suggesting that simple additive simulation using single-factor manipulations may overestimate the effects on soil C fluxes in the real world. Therefore, we propose that more multifactorial experiments should be considered in studying Earth systems.

The complete mitogenome of Hodgson's Red-Toothed Shrew, Episoriculus caudatus (Soricidae).

The Hodgson's Red-Toothed Shrew, Episoriculus caudatus belongs to the family Soricidae, and is widely distributed in northern South Asia, central and southern China and present in parts of northern Southeast Asia. In this study, the complete mitochondrial genome sequence of Episoriculus caudatus was determined. The mitogenome was 17,129 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with a base composition of 33.1% A, 29.2% T, 24.7% C, and 13.0% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Hodgson's Red-Toothed Shrew, Episoriculus caudatus.

The complete mitogenome of Asian Gray Shrews, Crocidura attenuata (Soricidae).

The Asian Gray Shrews, Crocidura attenuate, belongs to the family Soricidae. This widespread Asian species ranges from India and perhaps Pakistan in the west of its range, through much of eastern China and mainland Southeast Asia. In this study, the complete mitochondrial genome sequence of Crocidura attenuata was determined. The mitogenome is 17,534 base pairs in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region, with a base composition of 32.8% A, 31.8% T, 22.4% C and 13.0% G. The present study contributes to illuminating taxonomic status of Crocidura attenuata, and may facilitate further investigation of the molecular evolution of Soricidae.

The complete mitogenome of Chinese Mole Shrew, Anourosorex squamipes (Soricidae).

The Chinese Mole Shrew, Anourosorex squamipes belongs to the family Soricidae, and widely distributes in central and southern China, northern and south Burma, east India, northern Vietnam and Thailand. In this study, the complete mitochondrial genome sequence of Anourosorex squamipes was determined. The mitogenome is 17,121 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with base composition of 34.0% A, 31.3% T, 22.0% C, and 12.7% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Chinese Mole Shrew Anourosorex squamipes.

The complete mitogenome of Asiatic Short-tailed Shrew Blarinella quadraticauda (Soricidae).

The Asiatic Short-tailed Shrew, Blarinella quadraticauda, is an endemic shrew to China, and is only distributed in Sichuan. In this study, the complete mitochondrial genome sequence of B. quadraticauda was determined. The mitogenome is 17,014 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with a base composition of 33.3 % A, 31.8% T, 22.3% C and 12.6% G. This study contributes to illuminating taxonomic status of the Asiatic Short-tailed Shrew, B. quadraticauda.