Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Changes in the Habitat Preference of Crested Ibis (Nipponia nippon) during a Period of Rapid Population Increase.

ABSTRACT: The number of breeding pairs of crested ibis (Nipponia nippon) in Hanzhong, China has recovered remarkably from 2 to 511 from 1981 to 2019. Although the crested ibis has been closely monitored, the habitat preference of the bird has not been well studied despite the extensive increase in abundance. We used nest site data from the past 39 years and 30 environmental variables to develop species distribution models for each year. We applied random forest to select important environmental variables, and used logistic regressions to quantify the changes in habitat preferences in 39 years, taking into account the effects of interaction and quadratic terms. We found that six variables had strong impacts on nest site selection. The interaction term of rice paddies and waterbodies, and the quadratic term of precipitation of the wettest quarter of the year were the most important correlates of nest presence. Human impact at nest sites changed from low to high as birds increased their use of ancestral habitats with abundant rice paddies. We concluded that during the population recovery, the crested ibises retained their dependence on wetlands, yet moved from remote areas to populated rural regions where food resources had recovered due to the ban of pesticide use.

SUBMITTER: Ma L

PROVIDER: S-EPMC8465559 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Detection of Chlamydia psittaci and Chlamydia ibidis in the Endangered Crested Ibis (Nipponia nippon).

Project description:Chlamydia spp. are a group of obligate intracellular pathogens causing a number of diseases in animals and humans. Avian chlamydiosis (AC), caused by Chlamydia psittaci (C. psittaci) as well as new emerging C. avium, C. gallinacea and C. ibidis, have been described in nearly 500 avian species worldwidely. The Crested Ibis (Nipponia nippon) is a world endangered avian species with limited population and vulnerable for various infections. To get a better understanding of the prevalence of Chlamydia spp. in the endangered Crested Ibis, faecal samples were collected and analysed. The results confirmed that 20.20% (20/99) of the faecal samples were positive for Chlamydiaceae and were identified as C. ibidis with co-existence of C. psittaci in one of the 20 positive samples. In addition, ompA sequence of C. psittaci obtained in this study was classified into the provisional genotype Matt116, while that of C. ibidis showed high genetic diversity, sharing only 77% identity with C. ibidis reference strain 10-1398/6. We report for the first time the presence of C. ibidis and C. psittaci in the Crested Ibis, which may indicate a potential threat to the endangered birds and should be aware of the future protection practice.

| S-EPMC7019082 | biostudies-literature

Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon).

Project description:The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0-45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.

| S-EPMC6685491 | biostudies-literature

Decline of traditional rice farming constrains the recovery of the endangered Asian crested ibis (Nipponia nippon).

Project description:Traditional agriculture benefits a rich diversity of plants and animals. The winter-flooded rice fields in the Qinling Mountains, China, are the last refuge for the endangered Asian crested ibis (Nipponia nippon), and intensive efforts have been made to protect this anthropogenic habitat. Analyses of multi-temporal satellite data indicate that winter-flooded rice fields have been continuously reduced across the current range of crested ibis during the past two decades. The rate of loss of these fields in the core-protected areas has unexpectedly increased to a higher level than that in non-protected areas in the past decade. The best fit (R (2) = 0.87) numerical response model of the crested ibis population shows that a reduction of winter-flooded rice fields decreases population growth and predicts that the population growth will be constrained by the decline of traditional winter-flooded rice fields in the coming decades. Our findings suggest that the decline of traditional rice farming is likely to continue to pose a threat to the long-term survival and recovery of the crested ibis population in China.

| S-EPMC4646850 | biostudies-literature

Structure and polymorphism of the major histocompatibility complex class II region in the Japanese Crested Ibis, Nipponia nippon.

Project description:The major histocompatibility complex (MHC) is a highly polymorphic genomic region that plays a central role in the immune system. Despite its functional consistency, the genomic structure of the MHC differs substantially among organisms. In birds, the MHC-B structures of Galliformes, including chickens, have been well characterized, but information about other avian MHCs remains sparse. The Japanese Crested Ibis (Nipponia nippon, Pelecaniformes) is an internationally conserved, critically threatened species. The current Japanese population of N. nippon originates from only five founders; thus, understanding the genetic diversity among these founders is critical for effective population management. Because of its high polymorphism and importance for disease resistance and other functions, the MHC has been an important focus in the conservation of endangered species. Here, we report the structure and polymorphism of the Japanese Crested Ibis MHC class II region. Screening of genomic libraries allowed the construction of three contigs representing different haplotypes of MHC class II regions. Characterization of genomic clones revealed that the MHC class II genomic structure of N. nippon was largely different from that of chicken. A pair of MHC-IIA and -IIB genes was arranged head-to-head between the COL11A2 and BRD2 genes. Gene order in N. nippon was more similar to that in humans than to that in chicken. The three haplotypes contained one to three copies of MHC-IIA/IIB gene pairs. Genotyping of the MHC class II region detected only three haplotypes among the five founders, suggesting that the genetic diversity of the current Japanese Crested Ibis population is extremely low. The structure of the MHC class II region presented here provides valuable insight for future studies on the evolution of the avian MHC and for conservation of the Japanese Crested Ibis.

| S-EPMC4172706 | biostudies-literature

Spatial- and Temporal-Trajectory Analysis of the Crested Ibis (Nipponia nippon) by Fusing Multiple Sources of Data.

Project description:The Crested Ibis (Nipponia nippon) is an endangered animal with an extremely high ecological, humanistic, and scientific value. However, this species still faces survival challenges, due to rapidly shrinking foraging grounds, the serious interference of human behavior, and increased habitat requirements. Geographical environment is a significant factor affecting Crested Ibis behavior-pattern analysis and habitat protection. The spatial and temporal trajectory contains habitat location and period information, a vital record of the Crested Ibis' habits, and the basis of all research. Nevertheless, there are only a handful of studies on the missing trajectory data and fusing multiple sources of environmental data-research methods. We studied the spatial and temporal habitat use of the tracked Crested lbis by fusing multiple data-sources in China. This paper adopts the LSTM (long short-term memory) model to supplement the missing trajectory data and perform cluster mining; and a random forest model is used to predict the habitat of the Crested Ibis with high fitting accuracy (R2 = 84.9%). The results show that the Crested Ibis distribution-pattern is characterized by high altitude and proximity to woodland and rivers. Additionally, the habitat dependence on the village implicates human agricultural activities in positively impacting its reproduction. This paper provides a complete method for analyzing Crested Ibis' spatial and temporal trajectory by fusing multi-source data, which is crucial for protecting the survival and reproduction of the Crested Ibis.

| S-EPMC9854527 | biostudies-literature

How much can we trust GPS wildlife tracking? An assessment in semi-free-ranging Crested Ibis Nipponia nippon.

Project description:GPS tracking has been increasingly used for wildlife studies in recent decades, but its performance has not been fully assessed, especially for newly developed lightweight transmitters. We assessed the performance of eight GPS transmitters developed in China by attaching them to Crested Ibises Nipponia nippon confined to two acclimation cages mimicking real habitats. We calculated the distance between GPS locations and the centroid of the cages as the positioning error, and used the 95% (95th percentile) positioning errors to define the accuracy. The positioning success averaged 92.0%, which is much higher than that of previous studies. Locations were not evenly distributed by Location Class (LC), with the LC A and B locations accounting for 88.7%. The observed 95% positioning error in the locations of LC A (9-39 m) and B (11-41 m) was quite accurate, while up to 6.9-8.8% of poor-quality locations were detected in LC C and D with >100 m or even >1, 000 m positioning error. Positioning success and accuracy were different between the test sites, probably due to the difference in vegetation structure. Thus, we argue that the tested transmitters could provide a large proportion of high-quality data for fine-scale studies, and a number of poor-quality locations that need attention. We suggest that the HPOD (horizontal dilution of precision) or PDOP (positional dilution of precision) be reported instead of the LC as a measurement of location accuracy for each location to ensure identification and filtering of implausible locations.

| S-EPMC6063208 | biostudies-literature

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon).

Project description:Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.

| S-EPMC8382091 | biostudies-literature

Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon.

Project description:The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.

| S-EPMC3689774 | biostudies-literature