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BackgroundThe geese have strong broodiness and poor egg performance. These characteristics are the key issues that hinder the goose industry development. Yet little is known about the mechanisms responsible for follicle development due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to produce a comprehensive and integrated genomic resource and to better understand the biological mechanisms of goose follicle development.Methodology/Principal FindingsIn this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina). We obtained 67,315,996 short reads of 100 bp, which were assembled into 130,514 unique sequences by Trinity strategy (mean size = 753bp). Based on BLAST results with known proteins, these analyses identified 52,642 sequences with a cut-off E-value above 10−5. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcription changes during the goose laying/broodiness period using a tag-based digital gene expression (DGE) system. We obtained a sequencing depth of over 4.2 million tags per sample and identified a large number of genes associated with follicle development and reproductive biology including cholesterol side-chain cleavage enzyme gene and dopamine beta-hydroxylas gene. We confirm the altered expression levels of the two genes using quantitative real-time PCR (qRT-PCR).Conclusions/SignificanceThe obtained goose transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development and productivity.

Host species diversity can affect disease risk, but the precise nature of this effect is disputed. To date, most studies on the diversity–disease relationships have focused on host species richness and single diseases, ignoring phylogenetic diversity and disease richness. We first evaluated the effects of wildlife assemblage variables (i.e. species richness of wild ungulates and carnivores, phylogenetic structure) and livestock host density on the regional occurrence of 19 individual livestock diseases in Africa. We then explored the relationships between wildlife assemblage variables and the total disease burden (measured as disease richness) at regional scale across the entire continent of Africa. Our results suggest that wild ungulate and carnivore species richness had a positive relationship with disease richness, but no relationship with disease occurrence. When controlling for host species richness, standardized phylogenetic divergence was negatively correlated with both disease richness and disease occurrence while standardized phylogenetic richness was positively correlated with disease occurrences. Our results suggest that the phylogenetic structure of the surrounding wildlife assemblage can shape patterns of livestock diseases in Africa. Species richness alone is apparently inadequate for analyses of disease–diversity relationships, and this shortfall might partly account for current disagreements over the importance of the dilution effect. Future studies on this topic should strive to include parameters that take host phylogeny into account. A plain language summary is available for this article.

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long‐distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related. Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental‐scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity. Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence. Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.

Aim Although assembly processes have been studied in a wide range of taxa, determining assembly rules remains controversial, particularly in assemblages consisted of species with strong dispersal capacities. Moreover, few studies focused on communities in recently human‐created habitats. We tested two prevailing but opposing hypotheses, environmental filtering and limiting similarity, in waterbird communities across subsidence wetlands created by underground coal mining in China, with an aim to better understand assembly processes in communities composed of highly mobile species in human‐dominated landscape. Location The North China Plain. Methods We quantified taxonomic, functional and phylogenetic diversity of the waterbird assemblages in different seasons and compared the mean pairwise distances (MPD) and the mean nearest taxon distances (MNTD) with null models to examine whether co‐occurring species were clustered or overdispersed on the functional dendrogram or phylogenetic tree. Independent contributions of multi‐scale habitat variables therein were determined using a hierarchical partitioning method. Results We showed asynchronous patterns of seasonal dynamics among the multiple diversity metrics, with highest species diversity during autumn migration. Generally, the co‐occurring species were functionally and phylogenetically clustered. Habitat variables had stronger effects on the functional structure than on the phylogenetic structure of the communities. The degree of functional clustering increased in older and larger wetlands, while the assemblages shifted from functional clustering to overdispersion with increasing habitat diversity, landscape connectivity and human disturbance. Main conclusions The waterbird assemblages were mainly structured by environmental filtering, and the assembly processes were significantly affected by habitat variables, with stronger effects on functional diversity. Our study highlights the importance of environmental filtering and habitat variables in structuring assemblages dominated by species with high dispersal capacities and suggests that increasing habitat diversity and reducing disturbances will contribute to waterbird conservation in this human‐dominated landscape.