Yvonne I. Verkuil

The interplay between habitat availability and population differentiation

We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP.

Wind effects on prey availability: How northward migrating waders use brackish and hypersaline lagoons in the Sivash, Ukraine

Abstract Large numbers of waders migrating northward in spring use the Sivash, a large system of shallow, brackish and hypersaline lagoons in the Black Sea and Azov Sea region (Ukraine). The bottoms of these lagoons are often uncovered by the wind. Hence, for waders the time and space available for feeding depend on wind conditions. In hypersaline lagoons the benthic and pelagic fauna was very poor, consisting mainly of chironomid larvae (0.19 g AFDM·m −2 ) and brine shrimps Artemia salina , respectively. Brine shrimp abundance was correlated with salinity, wind force, wind direction and water depth. Dunlin Calidris alpina and curlew sandpiper Calidris ferruginea were the only species feeding on brine shrimp. As brine shrimp densities are higher in deeper water, smaller waders such as broad-billed sandpipers Limicola falcinellus are too short-legged to reach exploitable densities of brine shrimp. In brackish lagoons the benthic and pelagic fauna was rich, consisting of polychaetes, bivalves, gastropods, chironomid larvae, isopods and amphipods (8.9 to 30.5 g AFDM·m −2 ), but there were no brine shrimps. Prey biomass increased with the distance from the coast, being highest on the site that was most frequently inundated. Dunlin, broad-billed sandpiper and grey plover Pluvialis squatarola were the most abundant birds in the brackish lagoon. Due to the effects of wind-tides only a small area was usually available as a feeding site. Gammarus insensibilis was the alternative prey resource in the water layer, and their density varied with wind direction in the same way as brine shrimp. Curlew sandpipers and dunlins in the hypersaline lagoons and broad-billed sandpipers in the brackish lagoons often changed feeding sites, probably following the variation in prey availability. Only because of the large size and variety of lagoons are waders in the Sivash always able to find good feeding sites.

A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes).

Although the mitochondrial genome in birds has highly conserved features, with protein genes similar to mammals and amphibians, several variations in gene order around the hypervariable control region have been found. Here we report a novel gene arrangement around the control region in shorebirds (Charadriiformes). In ruffs Philomachus pugnax, the mitochondrial genome between cytochrome b and 12SrRNA was over 1.5 kb longer than reported for other Charadriiformes and contained a duplication of the control region together with NADH dehydrogenase subunit 6 (ND6) and the adjacent transfer RNAs: tRNA(Pro) and tRNA(Glu). Sequence data from 68 individuals from several stopover and breeding populations show that the duplication is widespread in ruffs. Similar gene re-arrangements have been found independently in unrelated tube-nosed seabirds and spoonbills.

Characterization of MHC class I in a long-distance migrant shorebird suggests multiple transcribed genes and intergenic recombination

The major histocompatibility complex (MHC) includes highly polymorphic gene families encoding proteins crucial to the vertebrate acquired immune system. Classical MHC class I (MHCI) genes code for molecules expressed on the surfaces of most nucleated cells and are associated with defense against intracellular pathogens, such as viruses. These genes have been studied in a few wild bird species, but have not been studied in long-distance migrating shorebirds. Red Knots Calidris canutus are medium-sized, monogamous sandpipers with migratory routes that span the globe. Understanding how such long-distance migrants protect themselves from disease has gained new relevance since the emergence of avian-borne diseases, including intracellular pathogens recognized by MHCI molecules, such as avian influenza. In this study, we characterized MHCI genes in knots and found 36 alleles in eight individuals and evidence for six putatively functional and expressed MHCI genes in a single bird. We also found evidence for recombination and for positive selection at putative peptide binding sites in exons 2 and 3. These results suggest surprisingly high MHC diversity in knots, given their demographic history. This may be a result of selection from diverse pathogens encountered by shorebirds throughout their annual migrations.

Spring migration of Ruffs Philomachus pugnax in Fryslan: estimates of staging duration using resighting data

Seasonal bird migration involves long flights, but most time is actually spent at intermediate staging areas. The duration of stay at these sites can be evaluated with mark—recapture methods that employ day-to-day local encounters of individually marked birds. Estimates of staging duration are based on two probabilities: the immigration probability, the complement of a birds seniority to an area, and the emigration probability, the complement of the staying probability. Estimating total staging duration from seniority and staying probabilities requires validation for resighting data and here we compare three data categories of Ruffs Philomachus pugnax passing through The Netherlands during northward migration: (1) newly colour-ringed, (2) previously colour-ringed and (3) radio-tagged Ruffs (recorded by automated receiving stations). Between 2004 and 2008, 4363 resighting histories and 95 telemetry recording histories were collected. As sample sizes for females were low, only data for males were analysed. Possible catching effects affecting estimates of staging duration were explored. Staying probability was estimated for all data. Seniority however, could not be estimated for newly marked Ruffs; the assumption of equal ‘capture’ probability for reverse-time models applied to estimate seniority is violated for seasonal resighting histories starting with a catching event. Therefore, estimates of total staging duration were based on resightings of previously colour-marked birds only. For radio-tagged birds a minimal staging duration (time between tagging and last recording) was calculated. Modelling indicated that newly colour-ringed birds had a higher staying probability than previously colour-ringed birds, but the difference translated to a prolonged staging duration in newly ringed birds of only 0.4–0.5 d, suggesting a very small catching effect. The minimal staging duration of radio-tagged birds validated estimates of staging duration for colour-ringed birds in 2007 but not in 2005. In 2005 a low resighting probability resulted in underestimates of staging duration. We conclude that (1) estimates of staying probability can be affected by catching although effects on staging duration might be small, and that (2) low resighting probabilities can lead to underestimates in staging duration. In our study previously ringed Ruffs resighted in 2006–08 yielded reliable estimates of staging duration as data had sufficiently high resighting probabilities. Average staging durations varied between 19 d in 2008 and 23 d in 2006.

Biometrics of Ruffs Philomachus pugnax migrating in spring through southern Belarus with special emphasis on the occurrence of ‘faeders’

In spring, the Ruff Philomachus pugnax passes through European inland sites in large numbers. Birds from eastern and western parts of the breeding range may differ in biometrics, but data on this species in eastern Europe are scarce. The aim of this study was to describe the biometrics of Ruffs migrating through southern Belarus in spring. In 2004, 242 birds were sexed by DNA analysis. Three birds sexed as males had female plumage but wing lengths intermediate between females and breeding‐plumage males, and were identified as cryptic males or ‘faeders’. Between 2001 and 2005, 2,237 Ruffs were ringed at the study site (1,310 males in breeding plumage, 911 females and 14 faeders). There was a strong seasonal variation in sex ratio. For adult Ruffs wing length was the best predictor of sex. Total head length and tarsusplus‐toe length distributions overlapped slightly between the sexes. There was evidence for slight bimodality in the distributions of wing, bill and tarsus‐plus‐toe length in non‐faeder males and in wing and bill length distributions for females. Mean wing lengths of Ruffs passing through the Belarus study site were similar to those birds from other locations in Europe and North Africa, but different from birds from South Africa, Yamal and the middle Lena River, suggesting that Ruffs have at least two different breeding populations.

A global threats overview for Numeniini populations: Synthesising expert knowledge for a group of declining migratory birds

The Numeniini is a tribe of 13 wader species (Scolopacidae, Charadriiformes) of which seven are Near Threatened or globally threatened, including two Critically Endangered. To help inform conservation management and policy responses, we present the results of an expert assessment of the threats that members of this taxonomic group face across migratory flyways. Most threats are increasing in intensity, particularly in non-breeding areas, where habitat loss resulting from residential and commercial development, aquaculture, mining, transport, disturbance, problematic invasive species, pollution and climate change were regarded as having the greatest detrimental impact. Fewer threats (mining, disturbance, problematic native species and climate change) were identified as widely affecting breeding areas. Numeniini populations face the greatest number of non-breeding threats in the East Asian-Australasian Flyway, especially those associated with coastal reclamation; related threats were also identified across the Central and Atlantic Americas, and East Atlantic flyways. Threats on the breeding grounds were greatest in Central and Atlantic Americas, East Atlantic and West Asian flyways. Three priority actions were associated with monitoring and research: to monitor breeding population trends (which for species breeding in remote areas may best be achieved through surveys at key non-breeding sites), to deploy tracking technologies to identify migratory connectivity, and to monitor land-cover change across breeding and non-breeding areas. Two priority actions were focused on conservation and policy responses: to identify and effectively protect key non-breeding sites across all flyways (particularly in the East Asian- Australasian Flyway), and to implement successful conservation interventions at a sufficient scale across human-dominated landscapes for species’ recovery to be achieved. If implemented urgently, these measures in combination have the potential to alter the current population declines of many Numeniini species and provide a template for the conservation of other groups of threatened species.

Non-breeding fæder Ruffs Philomachus pugnax associate according to sex, not morphology

Capsule Fæders (males that are female look-alikes) associate with males rather than females, at several different spatial scales. Aims To test the prediction that the occurrence in space and time of fæders on ecological grounds should track that of females. Methods The fraction of fæders was estimated in five morphometric data sets that were collected over four decades in four different countries in three different seasons (comprising 9133 Ruffs). The regression of fæder–female fractions was tested against the null model assuming that the number of fæders is 1.0% of females. Results The fraction of fæders in catches averaged 1.03%, varying between 0.3% in autumn in the UK up to 0.85% in Sénégal in winter and 1.04% in The Netherlands in spring. On a stopover in The Netherlands the fraction decreased from 1.3% to 0.7% when the females started to arrive. At all four spatial and temporal scales the regression of fæder–female fractions deviated from the null model: we found high fractions of fæders in catches with low fractions of females, indicating that fæders rather associate with the larger-sized ‘normal’ males. Conclusion We suggest that fæders spend the winter, and migrate with, the larger-sized lekking males, and we propose that any survival costs associated with the use of suboptimal habitats is compensated by higher reproductive success as sneakers on leks.

No evident spatial genetic structuring in the rapidly declining Black-tailed Godwit Limosa limosa limosa in The Netherlands

With 40% of the European Black-tailed Godwit population breeding in The Netherlands, this country harbours internationally significant numbers of this species. However, ongoing agricultural intensification has resulted in the fragmentation of the population and drastic population declines since 1967. By establishing genetic diversity, genetic differentiation and gene flow on the basis of 12 microsatellites, we investigated whether the population genetic structure of the Dutch Black-tailed Godwit bears the marks of these changes. Genetic diversity appeared to be moderate, and Bayesian model-based analysis of individual genotypes revealed no clustering in the Dutch populations. This was supported by pairwise FST values and AMOVA, which indicated no differentiation among the nine breeding areas. Gene flow estimates were larger than “one migrant per generation” between sample locations, and no isolation by distance was demonstrated. Our results indicate the maintenance of moderate levels of genetic diversity and genetic connectivity between breeding sites throughout the Dutch Black-tailed Godwit breeding population. We suggest that the Dutch Black-tailed Godwit breeding areas should be managed as a single panmictic unit, much as it is presently done.

Characterization of polymorphic microsatellite DNA markers in the black-tailed godwit (Limosa limosa: Aves)

We isolated and tested 16 microsatellite loci in black‐tailed godwits from the Netherlands (Limosa limosa limosa), and from Australasia (subspecies melanuroides). One locus was monomorphic, two loci had null‐alleles and one was significantly heterozygote deficient. The remaining 12 polymorphic loci had on average 7.9 alleles (range 5–11) and the mean expected heterozygosity was 0.69. No significant linkage disequilibrium between the loci was observed and all loci were autosomal. Fourteen loci were successfully cross‐amplified in bar‐tailed godwit (Limosa lapponica).