Southward migration and fuel deposition of Red Knots Calidris canutus

We compared the differences between spring and autumn in migration speed, fuelling rates and fuel loads of migrating Red Knots Calidris canutus. As a basis we used ringing data from Ottenby Bird Observatory, southeastern Sweden, collected 1948–2003, with morphometrical data from 1990–2003. Numbers ringed varied between 0 and 301 per year (average 56). Morphometrics, recoveries and recaptures of ringed birds indicated that most birds belonged to the Afro-Siberian subspecies C. c. canutus, possibly mixed with some Nearctic Red Knots C. c. islandica. Median trapping dates were 5 August (adults) and 31 August (juveniles). Mean body masses were low and almost equal for adults (111.8 g) and juveniles (111.4 g). The mean estimated fuel loads were 13–14% of lean body mass (LBM). In juveniles fuel loads increased with date. Among the few birds stopping over for longer than one day (2% of adults, 14% of juveniles), adult birds stayed on average 2.5 days and juveniles 3.4 days, with an overall average fuel deposition rate of 2.8% of LBM d–1. The autumn migration speed was estimated from ringing recoveries at 86 km d–1, which equals the speed of spring migration calculated from published information. The observed fuelling rate was as high as that of Red Knots at major spring stopover sites. We conclude that migration in autumn is as fast as in spring, although the generally small fuel loads indicate that migration is carried out in much smaller steps

Timing of spring migration in birds: long-term trends, North Atlantic Oscillation and the significance of different migration routes

We studied long-term trends and the yearly variation in mean spring passage time in 36 passerine bird species trapped at Ottenby Bird Observatory in south-eastern Sweden. Between the years 1952-2002, data were available for 22-45 years depending on species. Most long-distance migrant species passed progressively earlier over the study period (range: 2.5 days earlier to 0.7 days later per 10 years, with an average of 0.9 days earlier per 10 years). The annual variation in timing of migration in most species, regardless of migration distance, correlated negatively with the winter index of the North Atlantic Oscillation (NAO), a large-scale climate phenomenon influencing the climate in the North Atlantic region. Birds passed earlier after mild and humid winters., corresponding to the high phase of the NAO. This corroborates the pattern round at a nearby migration site with a comparable dataset (Helgoland, 600 km WSW of Ottenby). However, short/medium-distance migrant species at Otterby, in contrast to the situation at Helgoland, have shown no general trend of earlier passage in recent years. This was probably a consequence of the shorter study period at Ottenby, which included only the last 22-32 years (41 years at Helgoland), when the NAO showed no significant trend. At the species-specific level, the long-term trends in passage time were similar at the two sites, and there was some congruence to the extent that a given species was affected by NAO. Long-distance migrants wintering south and south-east of the breeding grounds showed some of the strongest changes in long-term trends (passing progressively earlier) at Ottenby, and for some of these species passage time varied negatively with NAO. Obviously, and contrary to previous suggestions, variations in NAO also influence birds migrating through eastern Europe, although the direct or indirect mechanisms through which this is achieved are unknown

First genetic data for the critically endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications

Funding Information: GMK and AK are grateful to staff, particularly Ianela García-Lau, Manolo Barro and volunteers at the Museo de Historia Natural ‘Felipe Poey’, La Habana, Cuba, for access to relevant specimens. This study was funded by University of Aberdeen (AB) and The Sound Approach Ph.D. Studentship (TJS).Peer reviewedPublisher PD

Evolutionary history of the Galápagos Rail Revealed by ancient mitogenomes and modern samples

The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.Fil: Chaves, Jaime A.. San Francisco State University; Estados Unidos. Universidad San Francisco de Quito; EcuadorFil: Martinez Torres, Pedro J.. Universidad San Francisco de Quito; EcuadorFil: Depino, Emiliano Agustín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Bio y Geociencias del NOA. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Museo de Ciencias Naturales. Instituto de Bio y Geociencias del NOA; ArgentinaFil: Espinoza Ulloa, Sebastian. University of Saskatchewan; Canadá. Pontificia Universidad Católica del Ecuador; EcuadorFil: García Loor, Jefferson. Universidad San Francisco de Quito; EcuadorFil: Beichman, Annabel C.. University of Washington; Estados UnidosFil: Stervander, Martin. Natural History Museum; Reino Unid

Phenology of the avian spring migratory passage in Europe and North America : Asymmetric advancement in time and increase in duration

Climate change has been shown to shift the seasonal timing (i.e. phenology) and distribution of species. The phenological effects of climate change on living organisms have often been tested using first occurrence dates, which may be uninformative and biased. More rarely investigated is how different phases of a phenological sequence (e.g. beginning, central tendency and end) or its duration have changed over time. This type of analysis requires continuous observation throughout the phenological event over multiple years, and such data sets are rare. In this study we examined the impact of temperature on long-term change of passage timing and duration of the spring migration period in birds, and which species' traits explain species-specific variation. Data used covered 195 species from 21 European and Canadian bird observatories from which systematic daily sampling protocols were available. Migration dates were negatively associated with early spring temperature and timings had in general advanced in 57 years. Short-distance migrants advanced the beginning of their migration more than long-distance migrants when corrected for phylogenic relatedness, but such a difference was not found in other phases of migration. The advancement of migration has generally been greater for the beginning and median phases of migration relative to the end, leading to extended spring migration seasons. Duration of the migration season increased with increasing temperature. Phenological changes have also been less noticeable in Canada even when corrected for rate of change in temperature. To visualize long-term changes in phenology, we constructed the first multi-species spring migration phenology indicator to describe general changes in median migration dates in the northern hemisphere. The indicator showed an average advancement of one week during five decades across the continents (period 1959-2015). The indicator is easy to update with new data and we therefore encourage future research to investigate whether the trend towards longer periods of occurrence or emergence in spring is also evident in other migratory populations. Such phenological changes may influence detectability in monitoring schemes, and may have broader implications on population and community dynamics.Peer reviewe

Surveillance of Influenza Virus A in Migratory Waterfowl in Northern Europe

Ducks may maintain influenza virus from 1 year to the next

Timing of spring migration in birds: long-term trends, North Atlantic Oscillation and the significance of different migration routes

We studied long-term trends and the yearly variation in mean spring passage time in 36 passerine bird species trapped at Ottenby Bird Observatory in south-eastern Sweden. Between the years 1952-2002, data were available for 22-45 years depending on species. Most long-distance migrant species passed progressively earlier over the study period (range: 2.5 days earlier to 0.7 days later per 10 years, with an average of 0.9 days earlier per 10 years). The annual variation in timing of migration in most species, regardless of migration distance, correlated negatively with the winter index of the North Atlantic Oscillation (NAO), a large-scale climate phenomenon influencing the climate in the North Atlantic region. Birds passed earlier after mild and humid winters., corresponding to the high phase of the NAO. This corroborates the pattern round at a nearby migration site with a comparable dataset (Helgoland, 600 km WSW of Ottenby). However, short/medium-distance migrant species at Otterby, in contrast to the situation at Helgoland, have shown no general trend of earlier passage in recent years. This was probably a consequence of the shorter study period at Ottenby, which included only the last 22-32 years (41 years at Helgoland), when the NAO showed no significant trend. At the species-specific level, the long-term trends in passage time were similar at the two sites, and there was some congruence to the extent that a given species was affected by NAO. Long-distance migrants wintering south and south-east of the breeding grounds showed some of the strongest changes in long-term trends (passing progressively earlier) at Ottenby, and for some of these species passage time varied negatively with NAO. Obviously, and contrary to previous suggestions, variations in NAO also influence birds migrating through eastern Europe, although the direct or indirect mechanisms through which this is achieved are unknown

On Speciation in Birds – Genomic Signatures across Space and Time

The process of speciation is a cornerstone in evolutionary biology. In Darwin’s On the Origin of Species, he described how he imagined that a new species would evolve to fill an empty niche. This focus on ecology shifted with Mayr towards the importance of isolation, and for many decades the geographic modes of speciation were debated. Speciation in sympatry, i.e. without any isolation between the diverging lineages, was controversial. Can speciation proceed in the face of gene flow, and if so, at what frequency? Lately, the perspective has shifted from the dichotomy of allopatry (i.e. non-overlapping distributions) and sympatry, in favour of investigating the processes involved in speciation, and acknowledging the role of ecology. In this thesis, I explore some of these aspects by studying several different groups of birds, some of which are distributed over three continents, and others that are confined to tiny, isolated, oceanic islands. Birds are highly mobile by nature, and in the absence of geographical barriers, a species is not likely to diverge without isolation, unless there is strong disruptive selection that can counteract the homogenizing effect of gene flow between incipient lineages. For this purpose, studying birds that are isolated on islands is particularly useful. I studied an interesting radiation of finches on Tristan da Cunha, which colonized the islands about four million years ago, but seemingly radiated into one pair of small-billed feeding generalists and large-billed feeding specialists in each of two islands, only a few hundred thousand years ago. I employed an array of genomic tools and uncovered the genetic target of natural selection on bill morphology. Interestingly, one of the two chromosomal regions with a large effect on bill morphology associated differently to small-billed and large-billed birds on the different islands. This supports the scenario that a small-billed ancestor colonized the two islands, and that the lineages then diverged in primary sympatry, in parallel processes on the two islands. This is not known to have happened in any other of the ten thousand species of birds described. Another case of speciation in sympatry, with selection overcoming gene flow, is the Gulf of Guinea seedeaters. Here, two separate colonizations from the same mainland source population led to secondary introgressive hybridization on São Tomé about a million years ago. My results suggest that this was followed by strong, asymmetric, ecological character displacement rendering one of the species an island giant that was previously not even recognized as a seedeater. Morphology was traditionally used as the basis for taxonomic classification, but my work has demonstrated that this is problematic for two opposite reasons. (1) The phenotypic differentiation is not proportional to genetic differentiation or time since divergence. This is illustrated by the relative similarity between blue tit populations on the Canary Islands, which have been isolated for several million years, and by the recent divergence between seedeaters on São Tomé and finches on Tristan da Cunha. On the other hand, (2) convergent evolution made two different Calandrella lark species, which are not each other’s closest relative, look so similar that they have hitherto been treated as the same species

Brief log of RADseq data processing, including custom scripts

Brief work log for analyses of RADseq data. I have used little snippets of custom scripts (which you are free to use and modify), but this log also makes use of plenty of neat little scripts made by other people. One script, by Shannon Hedtke, was modified to fit the purposes in this workflow, and that modified script is provided separately