The trans-Himalayan flights of bar-headed geese (Anser indicus).
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ABSTRACT:
SUBMITTER: Hawkes LA
PROVIDER: S-EPMC3111297 | biostudies-other | 2011 Jun
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Many birds wintering in the Indian subcontinent fly across the Himalayas during migration, including Bar-headed Geese (Anser indicus), Demoiselle Cranes (Anthropoides virgo) and Ruddy Shelducks (Tadorna ferruginea). However, little is known about whether shorebirds migrate across the Himalayas from wintering grounds beyond the Indian subcontinent. Using geolocators and satellite tracking devices, we demonstrate for the first time that Common Redshanks (Tringa totanus) and Whimbrels (Numenius phaeopus) wintering in Singapore can directly fly over the Himalayas to reach breeding grounds in the Qinghai-Tibet Plateau and north-central Russia respectively. The results also show that migratory shorebirds wintering in Southeast Asia can use both the Central Asian Flyway and the East Asian-Australasian Flyway. For Redshanks, westerly-breeding birds crossed the Himalayas while more easterly breeders on the Plateau migrated east of the Himalayas. For Whimbrels, an individual that crossed the Himalayas was probably from a breeding population that was different from the others that migrated along the coast up the East Asian-Australasian Flyway. The minimum required altitude of routes of trans-Himalayan Redshanks were no higher on average than those of eastern migrants, but geolocator temperature data indicate that birds departing Singapore flew at high elevations even when not required to by topography, suggesting that the Himalayan mountain range may be less of a barrier than assumed.
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Project description:Bar-headed geese (Anser indicus) are adaptable to plateau environments. In this study, we sequenced and assembled a high-quality chromosome-level genome of the bar-headed goose using PacBio long reads and Hi-C technique, and generated 115.73 Gb of Illumina short-reads and 95.89 Gb of PacBio long-reads. The assembled bar-headed goose genome, with a contig N50 of 5.734 Mb and a scaffold N50 of 65.77 Mb, is 1.129 Gb in length and includes 33 chromosomes and 451 fragments. BUSCO assessment yielded a completeness score of 94.4%. In total, 15,376 protein-coding genes were predicted, of which 94.95% had homologs in protein databases. We identified 78 positively selected genes (PSGs) in the bar-headed goose genome, which were mainly enriched in calcium ion and ATP-binding. This bar-headed goose genome will be an important resource for increasing our understanding regarding the genetic basis of adaptation to life at a high altitude.
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Project description:MHC class I proteins mediate functions in anti-pathogen defense. MHC diversity has already been investigated by many studies in model avian species, but here we chose the bar-headed goose, a worldwide migrant bird, as a non-model avian species. Sequences from exons encoding the peptide-binding region (PBR) of MHC class I molecules were isolated from liver genomic DNA, to investigate variation in these genes. These are the first MHC class I partial sequences of the bar-headed goose to be reported. A preliminary analysis suggests the presence of at least four MHC class I genes, which share great similarity with those of the goose and duck. A phylogenetic analysis of bar-headed goose, goose and duck MHC class I sequences using the NJ method supports the idea that they all cluster within the anseriforms clade.
| S-EPMC3036124 | biostudies-literature
Project description:The bar-headed goose is famed for migratory flight at extreme altitude. To better understand the physiology underlying this remarkable behavior, we imprinted and trained geese, collecting the first cardiorespiratory measurements of bar-headed geese flying at simulated altitude in a wind tunnel. Metabolic rate during flight increased 16-fold from rest, supported by an increase in the estimated amount of O2 transported per heartbeat and a modest increase in heart rate. The geese appear to have ample cardiac reserves, as heart rate during hypoxic flights was not higher than in normoxic flights. We conclude that flight in hypoxia is largely achieved via the reduction in metabolic rate compared to normoxia. Arterial [Formula: see text] was maintained throughout flights. Mixed venous PO2 decreased during the initial portion of flights in hypoxia, indicative of increased tissue O2 extraction. We also discovered that mixed venous temperature decreased during flight, which may significantly increase oxygen loading to hemoglobin.
| S-EPMC6721836 | biostudies-literature
Project description:Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird.
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Project description:Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries.
| S-EPMC4831473 | biostudies-literature
Project description:The first gut metagenome of wild Bar-headed geese
| PRJEB12153 | ENA
Project description:During the adaptive evolution of a particular trait, some selectively fixed mutations may be directly causative and others may be purely compensatory. The relative contribution of these two classes of mutation to adaptive phenotypic evolution depends on the form and prevalence of mutational pleiotropy. To investigate the nature of adaptive substitutions and their pleiotropic effects, we used a protein engineering approach to characterize the molecular basis of hemoglobin (Hb) adaptation in the high-flying bar-headed goose (Anser indicus), a hypoxia-tolerant species renowned for its trans-Himalayan migratory flights. To test the effects of observed substitutions on evolutionarily relevant genetic backgrounds, we synthesized all possible genotypic intermediates in the line of descent connecting the wildtype bar-headed goose genotype with the most recent common ancestor of bar-headed goose and its lowland relatives. Site-directed mutagenesis experiments revealed one major-effect mutation that significantly increased Hb-O2 affinity on all possible genetic backgrounds. Two other mutations exhibited smaller average effect sizes and less additivity across backgrounds. One of the latter mutations produced a concomitant increase in the autoxidation rate, a deleterious side-effect that was fully compensated by a second-site mutation at a spatially proximal residue. The experiments revealed three key insights: (i) subtle, localized structural changes can produce large functional effects; (ii) relative effect sizes of function-altering mutations may depend on the sequential order in which they occur; and (iii) compensation of deleterious pleiotropic effects may play an important role in the adaptive evolution of protein function.
| S-EPMC5903655 | biostudies-literature
Project description:BackgroundThe bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese.MethodsIn this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.Results10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.ConclusionWe reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.
| S-EPMC7144584 | biostudies-literature
Project description:The bar-headed goose (Anser indicus) has two black spots on its head. It is considered an important bird in China. It breeds in plateau lakes, especially saltwater lakes, and swamp areas. However, the intestinal flora of wild bar-headed geese in the Tibet Autonomous Region is currently not known. In this study, 16S rDNA sequencing was performed on the intestinal microbes of wild bar-headed geese. A total of 513,505 reads of raw data were obtained, and the results analyzed the average number of 128,376 ± 2,392 reads per sample. The microbiota of all samples consists of 10 main bacterial phyla, including Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Patescibacteria, Deferribacteres, Planctomy-cetes, Fusobacteria, and Tenericutes. The results indicated that Firmicutes (67.34%) was the predominant phylum, followed by Proteobacteria (29.03%) and Cyanobacteria (1.97%). In our research, we identified the intestinal flora of the wild bar-headed goose, which provides valuable information for further research on the gene function of the bar-headed goose and the intestinal flora of wild animals. These findings are also useful and valuable for genetic and high-altitude research in the Tibet Autonomous Region.
| S-EPMC8785396 | biostudies-literature