Spring migration of Ruffs Philomachus pugnax in Fryslân: 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 bird’s 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.

Genetic ‘accidents’ explain the origin of three male types in Ruffs <i>Philomachus pugnax</i>

Recentelijk verschenen in Nature Genetics twee artikelen over Kemphanen. Internationale onderzoeksteams hadden zich verdiept in de genetische achtergrond van Kemphanen vanwege hun unieke en complexe voortplantingssysteem met drie typen mannen: honkmannen, sa tellietmannen en faren. Deze mannen verschillen in uiterlijk, gedrag en fysiologie. Maar waarom blijven deze specifi eke kenmerken en het gedrag zo rigide gescheiden tussen deze drie types? In deze review beschrijven we hoe genetisch onderzoek, waar we zelf ook aan deelnamen, een verrassend antwoord vond.Recently two articles about Ruffs were published in Nature Genetics (Küpper et al. 2016, Lamichhaney et al. 2016). International teams mapped the genomes of Ruffs aiming to find an explanation for their peculiar and complex mating system with three types of males: independents, satellites and faeders. Ruffs show remarkable trait variation with each ornamented male sporting a unique plumage (van Rhijn 2014). However, within male types, plumage, behaviour, size and even physiology are strongly correlated. Why are these combinations of traits so rigidly fixed into just three male types? In the article we review the Nature Genetics studies, of which we were part of, and reveal surprising answers, opening new avenues for genetic and ecological studies

How wry is a wrybill?

The laterally asymmetrical bill of New Zealand’s endemic Wrybill Anarhynchus frontalis is unique among birds and has inspired much debate regarding its evolution and functional significance. Despite this, only one previous study has attempted to quantify the range of individual variation in bill shape, but used a single metric of curvature (bill tip angle). Using standardized digital photographs of 40 live Wrybills, we explored a range of metrics of bill length and curvature to describe the variation in bill shape in greater detail. Like the previous study, we found no sexual dimorphism in bill shape, despite males being slightly longer-billed than females, and recorded similar variation in bill tip angle (16–23°). However, we found that this single metric under-represented overall variation in bill shape, due to significant differences in where curvature began and was most pronounced along the length of the bill. Principal component analysis indicated that at least three independent metrics were required to describe the shape variation among individuals. Subtle differences in bill shape could plausibly affect an individual’s relative success among the range of Wrybill foraging strategies observed in breeding and non-breeding habitats. Elucidating the potential behavioral and fitness consequences of this variation will require detailed foraging and demographic studies with individuals of known bill morphology

Growth, maturity, and diet of the pearl whipray (<i>Fontitrygon margaritella</i>) from the Bijagós Archipelago, Guinea-Bissau

The pearl whipray Fontitrygon margaritella (Compagno & Roberts, 1984) is a common elasmobranch in coastal western African waters. However, knowledge on their life-history and trophic ecology remains limited. Therefore, we aimed to determine the growth, maturity and diet of F. margaritella from the Bijagós Archipelago in Guinea-Bissau. Growth was modelled with: von Bertalanffy, Gompertz and logistic functions. Model selection revealed no model significantly outperformed another. The sampled age ranged from less than 1 to 7 years (1.8 ± 1.9 cm, mean ± standard deviation) and size (disc width) ranged from 12.2 to 30.6 cm (18.7 ± 5.2 cm). Size-at-maturity was estimated at 20.3 cm (95% CI [18.8–21.8 cm]) for males and 24.3 cm for females (95% CI [21.9–26.5 cm]), corresponding ages of 2.2 and 3.9 years. The diet differed significantly among young-of-the-year (YOY), juveniles and adults (p = 0.001). Diet of all life stages consisted mainly of crustaceans (27.4%, 28.5%, 33.3%) and polychaetes (12.5%, 26.7%, 20.3%), for YOY, juveniles and adults respectively. This study shows that F. margaritella is relatively fast-growing, matures early and experiences ontogenetic diet shifts. These results contribute to status assessments and conservation efforts of F. margaritella and closely related species

Molecular identification of temperate Cricetidae and Muridae rodent species using fecal samples collected in a natural habitat

Molecular species identification from biological material collected at field sites has become an established ecological tool. However, extracting and amplifying DNA from degraded field samples, such as prey remains and feces that have been exposed to the elements, remains a challenge and costly. We collected 115 fecal samples of unknown small mammals, resembling fecal droppings of voles and mice (i.e., Cricetidae and Muridae), from a salt marsh in The Netherlands. We modified a previously published protocol into a relatively low-cost method with a PCR success of 95%. We demonstrate that species identification is possible for both Cricetidae and Muridae species using fecal samples of unknown age deposited in the field. For 90 samples, sequences of the variable control region in the mitochondrial genome were obtained and compared to published DNA sequences of small mammals occurring in north European salt marshes. A single sample, probably environmentally contaminated, appeared as Sus scrofa (n = 1). We positively identified house mouse Mus musculus, being the positive control (n = 1), and common vole Microtus arvalis (n = 88). In 81 sequences of 251 nt without ambiguous bases, ten haplotypes were present. These haplotypes, representing the central lineage of the western subspecies M. arvalis arvalis, were separated by 20 mutations from published control region haplotypes of the western European lineages sampled in France. Unlike earlier studies of cytochrome b variation in coastal European populations, we did not find indications of recent purging of genetic variation in our study area

Size, shape and sex differences in three subspecies of Black-tailed Godwits <i>Limosa limosa</i>

Capsule: Black-tailed Godwits Limosa limosa show sexual size dimorphism and size differences between the subspecies. The shape varies slightly between the subspecies, but not between the sexes. Aims: To investigate whether and how the three subspecies of Black-tailed Godwits, and the sexes of these subspecies, differ in size and shape. Methods: We collected body dimensions (lengths of the bill, total head, tarsus, tarsus-toe and wing) of adult Black-tailed Godwits from three locations (Iceland, the Netherlands and northwest Australia) corresponding to the breeding or wintering grounds of three known subspecies (islandica, limosa and melanuroides, respectively). Determining sex by molecular assays, we computed degrees of sexual size dimorphism. Using principal component analysis (PCA), we compared differences in size and shape among the different subspecies. Results: The limosa subspecies was the largest and also showed the most significant sexual size dimorphism. Sexual size dimorphism was smallest for wing length and largest for bill length. The first two axes of the PCA that included all subspecies of both sexes explained 94% of the total variation. Most body dimensions were highly correlated with each other, but wing length varied independently of the other dimensions. Males and females differed only in size (the first axis). However, one of the two small subspecies, islandica, also differed in shape (the second axis) from limosa and melanuroides. Conclusions: In all three subspecies of Black-tailed Godwits, females are larger than males. The fact that subspecies differed in the degree of size dimorphism and slightly in shape hints at sex-related differences in the ecological selection pressures between the different flyways

DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets:Validation with camera-recorded diets

Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free-living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole-nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size-adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera-recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R =.85 (95CI:0.68–0.94) at order level and at R =.75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds

Prenatal transfer of gut bacteria in Rock pigeon

Vertebrates evolved in concert with bacteria and have developed essential mutualistic relationships. Gut bacteria are vital for the postnatal development of most organs and the immune and metabolic systems and may likewise play a role during prenatal development. Prenatal transfer of gut bacteria is shown in four mammalian species, including humans. For the 92% of the vertebrates that are oviparous, prenatal transfer is debated, but it has been demonstrated in domestic chicken. We hypothesize that also non-domestic birds can prenatally transmit gut bacteria. We investigated this in medium-sized Rock pigeon (Columba livia), ensuring neonates producing fair-sized first faeces. The first faeces of 21 neonate rock pigeons hatched in an incubator, contained a microbiome (bacterial community) the composition of which resembled the cloacal microbiome of females sampled from the same population (N = 5) as indicated by multiple shared phyla, orders, families, and genera. Neonates and females shared 16.1% of the total number of OTUs present (2881), and neonates shared 45.5% of their core microbiome with females. In contrast, the five females shared only 0.3% of the 1030 female OTUs present. These findings suggest that prenatal gut bacterial transfer may occur in birds. Our results support the hypothesis that gut bacteria may be important for prenatal development and present a heritability pathway of gut bacteria in vertebrates