The Japanese murrelet (Synthliboramphus wumizusume) is a threatened bird endemic to Japan, Korea, and Russia. We generated the complete mitochondrial genome sequence to provide molecular genetic information for phylogeny and conservation of the species. The S. wumizusume mitochondrial genome is 16 714 bp in length and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, a non-coding control region, and a repeat region. Gene composition and order in the genome is consistent with that of other mitochondrial genomes of the order Charadriiformes currently available in the GenBank. Phylogenetic analysis using all available Charadriiform mitochondrial genomes revealed that interfamilial relationships of the birds based on mitochondrial genes were in agreement with those based on multilocus nuclear genes. The complete mitochondrial genome of S. wumizusume we sequenced might be a useful genetic resource for phylogenetic relationships, evolutionary biology, and conservation of the species.

Wind plays a significant role in the flight altitudes selected by nocturnally migrating birds. At mid-latitudes in the Northern Hemisphere, atmospheric conditions are dictated by the polar-front jet stream, whose amplitude increases in the autumn. One consequence for migratory birds is that the region’s prevailing westerly winds become progressively stronger at higher migration altitudes. We expect this seasonality in wind speed to result in migrants occupying progressively lower flight altitudes, which we test using density estimates of nocturnal migrants at 100 m altitudinal intervals from 12 weather surveillance radar stations located in the northeastern USA. Contrary to our expectations, median migration altitudes deviated little across the season, and the variance was lower during the middle of the season and higher during the beginning and especially the end of the season. Early-season migrants included small- to intermediate-sized long-distance migrants in the orders Charadriiformes and Passeriformes, and late-season migrants included large-bodied and intermediate-distance migrants in the order Anseriformes. Therefore, seasonality in the composition of migratory species, and related variation in migration strategies and behaviours, resulted in a convex–concave bounded distribution of migration altitudes. Our results provide a basis for assessing the implications for migratory bird populations of changes in mid-latitude atmospheric conditions probably occurring under global climate change.

The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

ABSTRACT Phylogenetic analysis of morphological data on 92 species in the order Charadriiformes showed that increased supraorbital ossification (SO) has evolved independently at least 4 times in this clade. Principal component analysis of size-corrected skeletal measures showed that an evolutionary increase in SO was associated with a body plan in which the cranium, humerus, and sternum were relatively large. A mass-corrected measure of the axial length of the eye was positively correlated with a mass-corrected measure of cranium length, both in the raw data and in phylogenetically independent contrasts. By revealing an association between the evolution of SO and increased relative size of the eye and flight-associated skeletal elements, these results support the hypothesis that an increased reliance on visually guided foraging in flight or diving has been a major selective factor favoring the evolution of increased SO in Charadriiformes.

In order to test for co-evolution of reproductive life history with body form, cluster analysis applied to nine skeletal measurements was used to identify three distinctive body types within the avian order Charadriiformes: a “sandpiper” type, a “gull/plover” type, and an “auk” type. Both in conventional analyses and in phylogenetically independent contrasts, the sandpiper body type was associated with increased values of a mass-adjusted measure of clutch volume and with decreased adult survival. A hypothesis that would explain the results is that increased reproductive effort characterizes charadriiform species with morphological features such as long bills and legs that render them vulnerable to predation, consistent with the hypothesis that reproductive effort represents a trade-off between current and future reproductive opportunities.

This survey was conducted from January 2013 to December 2013 to explore the avian fauna of Swat valley and to find out the major threats to the avian fauna of the area as it was neglected for years. Direct and indirect methods were used in the study by visiting the field and by interviewing the local peoples and hunters about the current and past status of the avian fauna of the area. During the current study direct and indirect methods were used. A total of 138 species were recorded belonging to 13 orders and 48 families. The order Passeriformes were recorded much in number that were 31 species. Most of the birds were migratory and few were resident. The fauna was very rich due to the flora of the area and also due to less hunting. Orders Anseriformes, Apodiformes, Charadriiformes, Columbiformes, Pelecaniformes, Phoenicopteriformes, and Psittaciformes were found migratory and orders Ciconiiformes, Coraciiformes, Galliformes, and Piciformes were found resident while some members of Gruiformes and Passeriformes were found migratory and some resident.

Development of an active risk-based surveillance strategy for avian influenza in Cuba

The present study was intended to record the biodiversity status of selected village ponds in district Hisar (Haryana) from August, 2012 to July, 2013. Periodic fortnightly visits were carried out to determine the species composition and distribution pattern of birds, phytoplankton and zooplankton. A total number of17 species of birds belonging to 9 orders (Anseriformes, Charadriiformes, Ciconiformes, Coraciifomes, Cuculiformes, Gruiformes, Passeriformes, Pelecaniformes and Psittaciformes) were identified in the study area. Charadriiformes was the most dominant order. The study revealed the presences of 18 species of phytoplankton belonging to Bacillariophyceae, Chlorophyceae, Cyanophyceae and Euglenophyceae. Bacillariophyceae having 7 species was found to be dominant among all. In case of zooplankton, 11 species were encountered of which 7 were Rotifers, 3 were Cladocera and 1 was Copepoda. Thus Rotifers represented the maximum number of species among zooplankton.

Avian influenza (AI) viruses have been isolated from a wide-diversity of free-living avian species representing several taxonomic orders. Isolations are most frequently reported from aquatic birds in the Orders Anseriformes and Charadriiformes, which are believed to be the primordial reservoirs for all AI viruses. Since first recognized in the late 1800s, AI viruses have been an important agent of disease in poultry and, occasionally, of non-gallinaceous birds and mammals. However, recent infections of humans with AI viruses, including highly pathogenic avian influenza (HPAI) H5N1 virus and low pathogenicity H7N9 AI virus in China during 2013, have increased the awareness of their potential to impact agricultural, wildlife, and public health. This chapter is intended to give general concepts and guidelines for planning and implementing surveillance programs for AI virus in wild birds.

Wild birds in the orders Anseriformes and Charadriiformes are the natural and asymptomatic reservoirs of influenza A viruses representing all of the avian hemagglutinin (HA) and neuraminidase (NA) subtypes. Transmission of avian influenza (AI) viruses from wild birds to gallinaceous poultry species occurs regularly and outcomes vary, ranging from asymptomatic infections to mortality. Circulation of H5 and H7 low pathogenic AI (LPAI) viruses in gallinaceous poultry may result in mutations in the HA protein cleavage site and the emergence of highly pathogenic AI (HPAI) viruses, which in poultry can cause severe disease with high economic losses. Since 2002, various wild bird species also have succumbed to infection with the Eurasian H5N1 HPAI viruses. The pathogenesis of AI is complex and the ability of these viruses to produce disease and death in avian species is dependent on various host, viral and environmental factors, which are not completely understood.

Paramyxoviruses and avian influenza viruses are present worldwide, and wild birds are known natural reservoirs of these viruses. This study monitored the circulation of these viruses in migratory and resident coastal birds captured in the state of Rio de Janeiro, Brazil. In total, 494 birds were trapped, and their fecal samples were collected and inoculated into embryonated chicken eggs. The allantoic fluids were evaluated using a hemagglutination test and PCR amplification of the genes of the M and L proteins of influenza A virus and paramyxovirus, respectively. Avian paramyxovirus was detected in 5 (1.01%) of the birds. The majority of these viruses were isolated from migratory birds classified into the order Charadriiformes (families Scolopacidae and Charadriidae). Four samples were characterized as avian paramyxovirus serotype-2 (APMV-2) by a hemagglutination inhibition test. These results reinforce the importance of continuous surveillance of wild species in Brazil.

Abstract Twelve birds species of the suborder Charadrii of the families Charadriidae, Recurvirostridae, Scolopacidae, Glareolidae were examined at Syvash Lake (Ukraine) in spring 2011. Cestodes were found in 82.1 % of examined birds. Seventeen cestode species of 6 families were found. Aploparaksis octacantha from Calidris alpinà and Echinocotyloides dubininae from C. ferruginea are new geographical records for the first time in Ukraine. Glareola pratincola is a new host record for Nadejdolepis paranitidulans. Cestodes of the genus Microsomacanthus were found in waders apparently due to the infection (2.8 %) in their intermediate hosts, gammarid crustaceans.

The present study is an attempt to analyse the reproductive success in Red Wattled Lapwing (Vanellus indicus) belonging to Order Charadriiformes, by comparing two nesting sites in Jammu. The nesting sites taken under consideration were open agricultural fields and the top of flat roofed buildings. The breeding season ranged from March to August with average clutch size of 3.53 ± 0.56 eggs (n=30) and an incubation period of 28-30 days. The most preferred site for nesting was found to be agricultural fields near some water source because of availability of food. In agricultural fields due to drying up of water source during peak summer, the scarcity in food resources for the young ones was noted thereby leading to the mortality of young ones of Red Wattled Lapwing, whereas it was also observed that on roof tops, eggs or hatchlings were easily predated by predators like monitor and the young ones were not able to land safely on the ground from such a height which caused their death.

The natural reservoirs for avian influenza virus (AIV) are wild bird species of the orders Anseriformes and Charadriiformes. The primary route of transmission for wild birds is through fecally contaminated surface water on shared aquatic habitats. A distilled water model has shown that AIV remains infectious in water for weeks to months with pH, salinity, and temperature affecting stability. To evaluate the effect of pH, salinity, and temperature on AIV persistence in natural surface water, we measured the duration of infectivity for two common low pathogenic AIV subtypes in 15 filtered surface water samples collected from major waterfowl habitats in Georgia, USA. Trials were performed at three incubation temperatures 10, 17, and 28 C. Consistent with previous studies, pH and temperature had a significant effect on the stability of AIV in filtered surface water. Both viruses were less stable at warmer temperatures and in acidic water (pH <5.0). Due to the limited range of salinity of the field water samples, the role of salinity in AIV stability in surface water could not adequately be evaluated. Variations in persistence times between water samples with comparable pH and salinities indicated that other factors affect AIV stability in natural surface water. These results contribute to the current understanding of AIV persistence in aquatic habitats and may help in identifying areas with an increased likelihood of AIV persistence and potential transmission.

Wild waterbirds sampled July 2006-September 2009 in Mongolia were tested for antibodies to avian influenza (AI) virus with the use of a commercially available blocking enzyme-linked immunosorbent assay. Antibodies were detected in 25% (572/2,282) of tested birds representing 26 species, and all antibody-positive samples were from 12 species in the orders Anseriformes and Charadriiformes. The highest antibody prevalence was in Ruddy Shelducks (Tadorna ferruginea; 61.7%; n=261; 95% confidence interval [CI] 55.8-67.6%), Whooper Swans (Cygnus cygnus; 38.4%; n=242; 95% CI 32.3-44.5%), Swan Geese (Anser cygnoides; 15%; n=127; 95% CI 8.6-21.4%), Bar-headed Geese (Anser indicus; 13%; n=738; 95% CI 10.3-15.1%), and Mongolian Gulls (Larus mongolicus; 3.9%; n=255; 95% CI 1.3-6.5%). There was no significant temporal or spatial variation in the presence of antibodies in the sampled species. However, Bar-headed Geese and Mongolian Gulls showed spatial variation in antibody prevalence in 2007 and 2008, respectively. Our study provides insights into the hatch year waterbirds' exposure to AI virus at their natal and molting sites in Mongolia.

During a 3-year surveillance study for avian influenza virus (AIV) infections at the Jeziorsko reservoir in central Poland, 549 oropharyngeal or cloacal swabs from 366 birds of 14 species belonging to 3 orders (Anseriformes, Charadriiformes and Gruiformes) were tested. AIV was detected in 14 birds (3.8%): Common Teals (12x), Mallard (1x) and Garganey (1x). Three potentially dangerous H5 AIV were detected in Common Teals (2x) and Garganey (1x) but all of them revealed a low pathogenic pathotype. A unique cleavage site amino acid motif PQREIR*GLF was found in one H5 isolate from a Garganey.

Virus isolation rates for influenza A virus (FLUAV) and Avian paramyxovirus serotype 1 (APMV-1) from wild bird surveillance samples are lower than molecular detection rates for the specific viral genomes. The current study was conducted to examine the possibility of increased virus isolation rates from real-time reverse transcription polymerase chain reaction (real-time RT-PCR) using alternative virus isolation substrates such as embryonating duck eggs (EDEs), embryonating turkey eggs (ETEs), Madin-Darby canine kidney (MDCK) cell cultures, and African green monkey kidney (Vero) cell cultures. Rectal swabs of birds in the orders Anseriformes and Charadriiformes were tested by real-time RT-PCR for the presence of FLUAV and APMV-1 genomes, and virus isolation (VI) was attempted on all real-time RT-PCR-positive samples. Samples with threshold cycle (Ct) ≤ 37 had VI rates for FLUAV of 62.5%, 50%, 43.8%, 31.5%, and 31.5% in embryonating chicken eggs (ECEs), ETEs, EDEs, MDCK cells, and Vero cells, respectively. A higher isolation rate was seen with ECEs compared to either cell culture method, but similar isolation rates were identified between the different embryonating avian eggs. Virus isolation rates for APMV-1 on samples with real-time RT-PCR Ct ≤ 37 were 75%, 100%, 100%, 0%, and 37.5% in ECEs, ETEs, EDEs, MDCK cells, and Vero cells, respectively. Significantly higher VI rates were seen with ECEs as compared to either cell culture method for all real-time RT-PCR-positive samples. Because of the limited availability and high cost of ETEs and EDEs, the data support the continuing usage of ECEs for primary isolation of both FLUAV and APMV-1 from real-time RT-PCR-positive wild bird surveillance samples.

The eight gene segments of avian influenza virus (AIV) reassort frequently and rapidly to generate novel genotypes and subtypes that are transmissible to a broad range of hosts. There is evidence that AIV can have a restricted host range and can segregate in space and time. Host-virus relationships at the species, geographic, and spatial scales have not been fully defined for AIV populations of the Pacific Flyway, particularly among the diverse waterfowl that occupy the Flyway in Alaska and California. Using the sequence analysis program Bayesian Tip-association Significance testing (BaTS) created for analysis of phylogeny-trait associations, we determined whether the genetic structure of Pacific Flyway AIVs sampled between 2006 and 2008 was influenced by the host species, geographic location of virus collection, and time of sampling. In posterior sets of trees, genetically similar viruses clustered by host species for thick-billed murres and glaucous gulls (order Charadriiformes), and for northern shovelers, northern pintails, and mallards (order Anseriformes). AIVs from Alaska and California were strongly spatially structured, clustering separately by region across all segments. The timing of sampling influenced the genetic structure of California AIV gene segments, possibly reflecting waves of host species movement into wintering areas. The strength of phylogeny-trait association varied by virus segment and by trait of interest, which we hypothesize is related to the frequent genetic reassortment and interspecies transmission in waterfowl.

Many species of colonial ground-nesting birds are known to be sensitive to predation by terrestrial predators. The response of prey under the pressure of predation can either be direct (depletion of prey) or indirect due to prey avoiding the predator. We studied the recolonization of arctic foxes into a large and growing breeding colony of lesser black-backed gulls. The gull colony reached the size of 20,000 pairs during the period of no foxes. The number of breeding gulls continued to increase after the colonization of foxes and reached a maximum of 40,000 pairs about 15 years later. During the same time period, the spatial coverage of the gull colony shrunk from 31.4 down to 18.6 km2, and the change in distribution was closely linked with position of fox dens, which ranged in number from one to three annually. In 2005, the number of breeding gulls decreased slightly with an ongoing shrinkage in spatial coverage. Food analyses from fox scats and stomachs showed that birds of the order Charadriiformes, particularly gulls, were the key prey item. Survival rates of gull nests were higher in the middle of the colony than at the colony edge close to a fox den. The colony area lost could be explained solely by the number of eggs removed by foxes but is unlikely, e.g., due to reclutching. We suggest that intraspecific predation contributes additionally to the effects of direct fox predation although to an unknown degree.

Summary1. Birds of marine environments have specialized glands to excrete salt, the saltglands. Located on the skull between the eyes, the size of these organs is expected to reflect their demand, which will vary with water turnover rates as a function of environmental (heat load, salinity of prey and drinking water) and organismal (energy demand, physiological state) factors. On the basis of inter‐ and intraspecific comparisons of saltgland mass (msg) in 29 species of shorebird (suborder Charadrii) from saline, fresh and mixed water habitats, we assessed the relative roles of organism and environment in determining measured msg species.2. The allometric exponent, scaling dry msg to shorebird total body mass (mb), was significantly higher for coastal marine species (0·88, N = 19) than for nonmarine species (0·43, N = 14). Within the marine species, those ingesting bivalves intact had significantly higher msg than species eating soft‐bodied invertebrates, indicating that seawater contained within the shells added to the salt load.3. In red knots (Calidris canutus), dry msg varied with monthly averaged ambient temperature in a U‐shaped way, with the lowest mass at 12·5 °C. This probably reflects increased energy demand for thermoregulation at low temperatures and elevated respiratory water loss at high temperatures. In fuelling bar‐tailed godwits (Limosa lapponica), dry msg was positively correlated with intestine mass, an indicator of relative food intake rates. These findings suggest once more that saltgland masses vary within species (and presumably individuals) in relation to salt load, that is a function of energy turnover (thermoregulation and fuelling) and evaporative water needs.4. Our results support the notion that msg is strongly influenced by habitat salinity, and also by factors influencing salt load and demand for osmotically free water including ambient temperature, prey type and energy intake rates. Saltglands are evidently highly flexible organs. The small size of saltglands when demands are low suggests that any time costs of adjustment are lower than the costs of maintaining a larger size in this small but essential piece of metabolic machinery.