Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds.

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

Morphological, molecular and histopathological characterization of Plagiorhynchus crassicollis (Acanthocephala: Plagiorhynchidae) from a neotropical shorebird in Patagonia, Argentina.

In this work we report Plagiorhynchus (Plagiorhynchus) crassicollis from Patagonia, Argentina. Specimens were collected from the small intestine of a charadriid shorebird with Neotropical distribution, the Two-banded Plover (Charadrius falklandicus). Both morphological and molecular characterization, plus pathological aspect of this species is provided. Plagiorhynchus (Plagiorhynchus) crassicollis is characterized by having a proboscis with 18-20 longitudinal rows of hooks and 11-14 hooks per row. Sequences of the small subunit (SSU) and large subunit (LSU) of the nuclear ribosomal DNA were obtained and compared with other sequences available in GenBank. Phylogenetic analyses inferred with each molecular marker consistently showed that P. (P.) crassicollis is sister taxa to Plagiorhynchus (Plagiorhynchus) aznari, a parasite of the long-billed curlew (Numenius americanus) from northern Mexico. Pathologic findings associated with the parasites include ulcerative enteritis, granulomatous inflammation, diffuse lymphocytic infiltration, serositis, and peritonitis. This record expands the host and geographical record of P. (P.) crassicollis, provide baseline information on its pathological aspects, and represents the first molecular characterization of P. crassicollis in the Neotropics.

Louse Flies of Charadrii and Scolopaci Shorebirds Migrating through Central Europe.

Louse flies are blood-sucking ectoparasites of birds and mammals of veterinary and medical importance. These flies damage host skin and serve as vectors for blood-associated pathogens. Little is known about their phenology, host selection, and prevalence in wild birds. Our study provided a broad-scale assessment of louse flies parasitizing Charadrii and Scolopaci shorebirds during their migration through Central Europe. We collected louse flies from 3,129 specimens in 22 species of shorebirds at a major migratory stopover site in central Poland in 2011-17. In total, 31 Ornithomya avicularia and 15 Ornithomya chloropus specimens occurred on five wader species: Common Snipe (Gallinago gallinago), Ruff (Calidris pugnax), Dunlin (Calidris alpina), Curlew Sandpiper (Calidris ferruginea), and Wood Sandpiper (Tringa glareola). Prevalences ranged from 0.23% to 4.62%. No individual birds were infested by both species of fly, and no flies were found on an additional 17 wader species. The rarer of the two flies, O. chloropus, occurred on all infested bird species, whereas O. avicularia occurred only on Common Snipe and Curlew Sandpiper. In comparison with the other four infested wader species, Common Snipe (n=1,194) was more frequently infested with O. avicularia than with O. chloropus. Our study shows that the prevalence of louse flies on shorebirds is much lower than on other avian taxa. Ecologic and evolutionary mechanisms leading to the relative rarity of louse flies on shorebirds remain to be understood.

The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii.

The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii's mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.

Clutch size limitation in waders: experimental test in redshank Tringa totanus.

Several hypotheses have been raised to explain the upper limit of clutch size at four eggs in waders (suborder Charadrii), which may play an important role in the evolution of the variety of mating and parental care systems in this group. Experimental tests of the hypotheses have produced conflicting results. It was recently suggested that the combined effects of several incubation costs of a larger clutch suffice to limit its size to four eggs in this group. Here we test the incubation-limitation hypothesis in a field experiment, in redshank Tringa totanus. We created five-egg clutches by adding one egg from another nest to a just completed four-egg clutch. Four-egg control clutches were created by replacing one of the eggs by an egg from another nest. All egg removals, additions and replacements were done before incubation started. Incubation time in five-egg clutches increased by 1 day to 24.3±0.23 days, compared to 23.3±0.32 days in four-egg clutches. Egg hatchability and nest predation rates did not differ significantly between treatments. On average five-egg clutches produced one extra chick at hatching (4.5±0.26 chicks) compared to four-egg clutches (3.5±0.27 chicks). Also when several additional costs from incubating enlarged clutches are added, redshanks by laying a fifth egg would on average increase their reproductive success at hatching by an estimated 22%. The incubation-limitation hypothesis therefore is clearly rejected in this species. Possible mechanisms behind the four-egg clutch limit in waders and ways of testing the alternatives are discussed.