Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications.

BACKGROUND: The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. RESULTS: In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals. CONCLUSIONS: This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations.

Metagenomic and Antibiotic Resistance Analysis of the Gut Microbiota in Larus relictus and Anatidae Species Inhabiting the Honghaizi Wetland of Ordos, Inner Mongolia, from 2021 to 2023.

Gut microbes thrive by utilising host energy and, in return, provide valuable benefits, akin to a symbiotic relationship. Here, metagenomic sequencing was performed to characterise and compare the community composition, diversity and antibiotic resistance of the gut microbiota of Relict gull (Larus relictus) and Anatidae species. Alpha diversity analysis revealed that the intestinal microbial richness of L. relictus was significantly lower than that of Anatidae, with distinct differences observed in microbial composition. Notably, the intestines of L. relictus harboured more pathogenic bacteria such as clostridium, which may contribute to the decline in their population and endangered status. A total of 117 strains of Escherichia coli were isolated, with 90.60% exhibiting full susceptibility to 21 antibiotics, while 25.3% exhibited significant biofilm formation. Comprehensive Antibiotic Resistance Database data indicated that glycopeptide resistance genes were the most prevalent type carried by migratory birds, alongside quinolone, tetracycline and lincosamide resistance genes. The abundance of resistance genes carried by migratory birds decreased over time. This metagenomic analysis provides valuable insights into the intestinal microbial composition of these wild bird species, offering important guidance for their conservation efforts, particularly for L. relictus, and contributing to our understanding of pathogen spread and antibiotic-resistant bacteria.

Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China.

The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases.

Development of integrated wetland change detection approach: In case of Erdos Larus Relictus National Nature Reserve, China.

Wetlands are threatened by the global warming and the human exploitation pressure, and have been shrinking quickly in recent years. Timely and accurate wetland area change detection is the primary task for wetland conservation and restoration. The objective of this study is to develop an integrated change detection approach which integrates the advantages of spectral mixture analysis (SMA) and change vector analysis (CVA) for the change identification of wetland dynamics. In the proposed approach, water, vegetation and soil fractions of wetlands were derived by SMA; then, the detailed change information (including change magnitude and 12 change direction categories) were calculated through CVA. The proposed approach was applied for the wetlands change in Erdos Larus Relictus National Nature Reserve (ELRNNR), China, using time-series Landsat images during 1977-2017. We found that the wetland faced serious degradation, with water fraction changed to soil (5.79 km2), to vegetation (1.35 km2) and to both soil and vegetation (3.53 km2). From 1977 to 2000, a slight degradation occurred in the northeast edge of Bojiang Lake and a marginal degradation in Bojiang and Houjia Lakes inside the ELRNNR, with water fraction changed to soil and vegetation. During 2000-2010, severe degradation occurred in ELRNNR, and from 2010 to 2017, the wetland was more susceptible to the precipitation change and human activities. Analysis of the result indicated that the long-term drought and effects of mismanagement as well as misuse by human beings were the driving factors of wetland degradation. The proposed approach in this study achieves a higher accuracy than the classification approach to detect wetland change, with the ability to obtain more detailed change information.

Seasonal dispersal and longitudinal migration in the Relict Gull Larus relictus across the Inner-Mongolian Plateau.

The Relict Gull Larus relictus is a globally vulnerable species and one of the least known birds, so understanding its seasonal movements and migration will facilitate the development of effective conservation plans for its protection. We repeatedly satellite-tracked 11 adult Relict Gulls from the Ordos sub-population in Hongjian Nur, China, over 33 migration seasons and conducted extensive ground surveys. Relict Gulls traveled ∼800 km between Hongjian Nur in northern China to the coast of eastern China in a predominantly longitudinal migration, following a clockwise loop migration pattern. The gulls migrated faster in spring (4 ± 2 d) than in autumn (15 ± 13 d) due to a time-minimization strategy for breeding, and they showed considerable between-individual variation in the timing of the autumn migration, probably due to differences in the timing of breeding. Gulls that made at least two round trips exhibited high flexibility in spring migration timing, suggesting a stronger influence of local environment conditions over endogenous controls. There was also high route flexibility among different years, probably due to variations in meteorological or habitat conditions at stopover sites. Relict Gulls stayed for a remarkably long time (234 ± 17 d) on their major wintering grounds in Bohai Bay and Laizhou Bay, between which there were notable dispersals. Pre-breeding dispersals away from the breeding area were distinct, which seemed to be a strategy to cope with the degradation of breeding habitat at Hongjian Nur. Overwhelming lake shrinkage on the breeding ground and at stopover sites and loss of intertidal flats on the wintering grounds are regarded as the main threats to Relict Gulls. It is crucial to make protection administrations aware of the great significance of key sites along migration routes and to promote the establishment of protected areas in these regions.

Complete mitochondrial genome of Relict Gull, Larus relictus (Charadriiformes: Laridae).

The complete mitochondrial genome sequence of Larus relictus was 16,586-bp long, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region. Most PCGs begin with the typical ATN start codon with the exception of COI and ND5 genes, which use GTG as the initiation codon. Stop codons AGG, TAG, TAA and AGA are present in the PCGs; exceptions are COIII and ND4, which possess incomplete termination codons (T), and ND3, in which one extra C nucleotide is found. Secondary structure prediction of the 22 tRNA genes revealed the absence of the DHU arm in tRNA(Ser)((AGN)). Seven conserved sequence box elements, as well as the origin of H-strand replication (OH) and bidirectional light- and heavy-strand transcription promoters (LSP/HSP), are found in control region.

Preliminary study of genetic diversity and population structure of the Relict Gull Larus relictus (Charadriiformes Laridae) using mitochondrial and nuclear genes.

The genetic diversity and the population history of the Relict Gull (Larus relictus) were studied based on the sequences of two mitochondrial genes (Cyt b and ND2) and one nuclear gene (the third intron of the Z-linked muscle-specific kinase gene [MUSK]) from 47 individuals. The results showed that the population expresses very low genetic diversity while lacking large geographical population. Demographic history analysis suggested that population expansion might have been recent and that the average estimated expansion time of L. relictus is from 0.09 to 0.23 Ma BP. Whether the other three breeding subpopulations are involved in the Ordos breeding subpopulation, require further study with more effective molecular markers. The species is threatened by habitat loss and fragmentation, and actions to protect it are suggested to improve the population fragmentation of breeding.

Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae.

The structure of the mitochondrial DNA control region in the Relict Gull (Larus relictus) was predicted and compared with data from the National Center for Biotechnology Information (NCBI) on five other gulls. The results showed that the control regions of the six gulls comprise three domains. Sequences of CSB-1-like (domain I) and CSB-1 (domain III) in L. relictus have the highest similarity with those in the other five gulls. The insertion fragments are located in downstream domain I of L. ridibundus, L. brunnicephalus, and L. saundersi. Seven conserved sequence boxes (additional box, F-box, E-box, D-box, C-box, bird-similarity-box, and B-box) are located in domain II in all six gulls. It is suggested that the CSB-2/3 sequence, the origin of H-strand replication, and bidirectional light- and heavy-strand transcription promoters in domain III of L. relictus have some distinguishing features to those of other gulls. Some repeat units are contained in the 3' end of the control region in the five gulls; however, no repeat units are found in the sequence CAAACAACAAA in L. relictus. The distribution of nucleotide diversity analysis will provide the useful information on the selected DNA fragment within the control region for genetic analyses among gulls.