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Thursday, 27 February 2014

Popular article from the The Auk journal: Using geolocators for migration studies in birds.

New Discoveries in Landbird Migration using Geolocators, and a Flight Plan for the Future

The Auk 130(2):211-222. 2013


Emily A. McKinnon ,1 
Kevin C. Fraser
Bridget J. M. Stutchbury
Department of Biology, York University, Toronto, Ontario M3J2S5, Canada
1 E-mail: emilymck@yorku.c


One of the most read articles from the Auk journal, and a great summary of the trend in using miniaturized geolocation devices to track bird migration.

Link to pdf.

Summary Figure

Figure Legend
Since their deployment on the first migratory landbirds in 2007, geolocators have been used to track individual birds in the Palearctic-Tropical, Nearctic-Neotropic, and Austral migratory systems. Colors that frame the photographs match the colors that indicate migratory routes. One individual's spring migration is shown for each subspecies (two subspecies are shown for Purple Martin and Swainson's Thrush, and three for Northern Wheatear), except for Fork-tailed Flycatcher (yellow) and Thrush Nightingale (bright green), whose fall migrations are shown. Photo credits: Red-eyed Vireo, Wood Thrush, and Veery: Lang Elliot; Swainson's Thrush: Darren Irwin; Red-backed Shrike: Per Eckberg; Purple Martin and Fork-tailed Flycatcher: Harold Stiver; Yellow-billed Cuckoo: Karthryn Mann; Snow Bunting: Sebastien Descamps; Northern Black Swift: Steven Daly; Common Swift: Steve James; Eurasian Hoopoe, Northern Wheatear, and Thrush Nightingale: Mikkel W. Kristensen.

Wednesday, 26 February 2014

Great Tit genetic analysis of UK and The Netherlands populations reveals subtle patterns of species level evolution

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Heredity (2014) 112, 307–316; doi:10.1038/hdy.2013.107; published online 23 October 2013

K van Oers 1,6
AW Santure 2,6
I De Cauwer 2,3,6
NEM van Bers 1,4
RPMA Crooijmans 4
BC Sheldon 5
ME Visser 1
J Slate 2
MAM Groenen 4

1 Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
2 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
3 Laboratoire de Genetique et Evolution des Populations Vege ́tales, UMR CNRS 8198, Batiment SN2, Universite des Sciences et Technologies de Lille - Lille 1, Villeneuve d’Ascq Cedex, France
4 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, The Netherlands
5 Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
6 These authors contributed equally to this work.
Correspondence: Dr K van Oers, Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands. E-mail:

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life- history evolution. Linkage maps provide a valuable tool for the unravelling of such trait - gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the Great Tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch (Taeniopygia guttata), chicken (Gallus gallus) and the green anole lizard (Anolis carolinensis) genomes provided further insight into the evolution of avian karyotypes.

In this study, the authors describe two high-density whole-genome linkage maps of the Great Tit (Parus major), constructed using a set of SNP markers originating from a 9193 SNP Illumina iSelect BeadChip. They genotyped a captive F2 inter-cross population from the Netherlands Institute of Ecology (NIOO-KNAW; n=398), and birds from a wild study population (Wytham Woods; n=1656) near Oxford, UK. 
Studying replicate genetic maps for two independent populations was extremely beneficial and led to the following conclusions:
 Linkage maps produced by two different methods showed that there were no marker inconsistencies at linkage group level (that is, no marker was present on a specific linkage group on one map and present on another linkage group on the other map), and that within the linkage groups there was high consistency between the marker orders in the two populations.
 As linkage group sizes were similar between the wild and captive populations it was suggested that there was no population specific variation in recombination rates across chromosomes.
 The heterogametic sex (females in birds) is hypothesised to have a shorter genetic map due to less recombination however this was not found to be case in these Great Tits. Surprisingly though evidence was found for small differences in recombination rates between sexes (heterochiasmy) that was consistent within and between chromosomes, and across the two populations (see article Figure 3 below).
 Numerous intrachromosomal rearrangements were found when comparing the Great Tit genome to that of the Chicken suggesting that these were genuine evolutionary differences.

Figure 3 (representative cropped section)
Size Dimorphism Index (SDI, y-axis) calculated for windows of 20 SNP markers (marker order, x-axis) on the NL (orange) and UK (blue) framework maps. Positive SDI indicates that female recombination rates within the 20 SNP window was higher; negative values indicate greater recombination rates in males.

Authors Conclusions
"In conclusion, we have constructed high-density linkage maps of two independent great tit populations. The maps will be valuable resources to aid with quantitative trait loci mapping, genome-wide association studies and chromosome partitioning of quantitative genetic variation. More fundamentally, we show that replicated maps constructed using the same SNPs reveal new insight into bird karyotype evolution; in particular a hitherto undetected degree of fine scale heterochiasmy that opens up an exciting new opportunity to study the evolution and fitness consequences of heterochiasmy."

Saturday, 22 February 2014

Variation of annual migratory timings in Hudsonian Godwits does not accumulate detrimental effects in breeding success or survival

Article Title
An Exception to the Rule: Carry-Over Effects Do Not Accumulate in a Long-Distance Migratory Bird

Nathan R. Senner, 1
Wesley M. Hochachka, 1
James W. Fox, 2
Vsevolod Afanasyev, 2

1. Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America
2. British Antarctic Survey, Cambridge, United Kingdom

PLoS ONE 9(2): e86588. doi:10.1371/journal.pone.0086588

Recent years have seen a growing consensus that events during one part of an animal’s annual cycle can detrimentally affect its future fitness. Notably, migratory species have been shown to commonly display such carry-over effects, facing severe time constraints and physiological stresses that can influence events across seasons. However, to date, no study has examined a full annual cycle to determine when these carry-over effects arise and how long they persist within and across years. Understanding when carry-over effects are created and how they persist is critical to identifying those periods and geographic locations that constrain the annual cycle of a population and determining how selection is acting upon individuals throughout the entire year. Using three consecutive years of migration tracks and four consecutive years of breeding success data, we tested whether carry-over effects in the form of timing deviations during one migratory segment of the annual cycle represent fitness costs that persist or accumulate across the annual cycle for a long-distance migratory bird, the Hudsonian godwit, Limosa haemastica. We found that individual godwits could migrate progressively later than population mean over the course of an entire migration period, especially southbound migration, but that these deviations did not accumulate across the entire year and were not consistently detected among individuals across years. Furthermore, neither the accumulation of lateness during previous portions of the annual cycle nor arrival date at the breeding grounds resulted in individuals suffering reductions in their breeding success or survival. Given their extreme life history, such a lack of carry-over effects suggests that strong selection exists on godwits at each stage of the annual cycle and that carry-over effects may not be able to persist in such a system, but also emphasizes that high-quality stopover and wintering sites are critical to the maintenance of long-distance migratory populations.

The authors present results from a study to look for the accumulation and dissipation of carry-over effects across an entire annual cycle, using data from 26 adult Hudsonian godwits (Limosa haemastica) from the Beluga River region in Alaska. The birds carried British Antarctic Survey geolocation-tracking devices that recorded data from three consecutive years of migration (2009-2011). These data were then compared with four consecutive years of data on breeding success, measured as producing young living to past 28 days. 

Godwits migrate the entire length of the Western Hemisphere: Beluga River - breeding site; central Saskatchewan - staging site during southward migration; Amazon Basin, Colombia - stopover site during southward migration; Buenos Aires Province, Argentina - stopover site during southward migration; Isla Chiloe, Chile - nonbreeding site; and Rainwater Basin, Nebraska - staging site during northward migration (see Figure 1). They then must breed within a short, nine-week summer. This constrained time-frame was therefore thought likely to be affected by delays in migration which may in turn increase the likelihood of detrimental carry-over effects on events such as nesting. 

The authors predicted that the godwits falling behind during one portion of their annual cycle would either not recoup this lost time or would  subsequently fall further behind, resulting in a late arrival on the breeding grounds, and a failure to produce a new brood.

Figure 1.
Map showing the migration routes of Hudsonian godwits breeding at Beluga River, Alaska. Twenty-six individuals were tracked across three years 2009–2012. Each red triangle denotes the location of an individual on one day, but does not necessarily indicate that the individual stopped in that location. Each blue circle denotes a region in which the majority of godwits stopped and congregated in both years.

Figure 2 shows the variation in timing of arrival and departure from the migration points, used as a measure of carry over effect. Each bar represents the average relative difference in timing of departure or rates of change for all individuals migrating either ahead or behind the population mean.

This is one of the first studies to document how individual birds of a migratory species control carry-over effects due to delays in the timing of migration events, by analysing changes in reproductive success and survival. The authors found that in spite of having one of the most extreme migrations of any migratory bird, returning godwits that migrated later than the population mean during one portion of their annual cycle did not remain behind for the entirety of their annual cycle, nor did they suffer reduced breeding success or survival.

Wednesday, 19 February 2014

Birds and the UK 2014 floods - BBC News article 17th February 2914


Wildlife organisations are being very careful in assessing the impacts of the recent flooding on species and the environment.
"We are not saying this is a disaster or this is something where wildlife has really suffered," Grahame Madge from the RSPB told me, keenly aware that when people's lives and homes are being threatened by rising waters, concerns about animal life comes a distant second.
Certainly the December storms and tidal surges had potentially very serious implications for many coastal habitats and species.
report drawn up by Natural England showed that over 40 Sites of Special Scientific Interest (SSSIs) in England had been affected.
However, the impact of the unprecedented downpours on the Somerset Levels, the Thames and the Severn is much harder to gauge.
Birds and animals should in many cases be able to move away from relatively slow rising river floods, unlike tidal surges.
However, there are worries about some small mammals, particularly hedgehogs, who are hibernating at this time of year. The RSPB expects that many of those caught in flooded areas will drown.
Dabbling ducks will also face problems.
These are water birds that love to stick their bottoms in the air as they up-end in the shallow reaches searching for food.
Mallards, teals and pintails are common on the Somerset Levels but according to Grahame Madge, the floods will have made it difficult for them to feed.
"These are a group of ducks that take food from the few inches at the top of the water column, when it is too deep beyond their dabbling ability they have to move on to other sites," he said.
The RSPB suspects that many of these ducks have moved on to other, more inaccessible sites in the Levels but the floods are making it very difficult for their counters to get out and make certain.
Another bird struggling in the ongoing wet conditions is the Kingfisher. You might be forgiven for thinking that with all the water about, these fish loving brightly coloured fellows would be in their element.
Sadly, that would be short-sighted.
"They suffer when you get a high silt load in the water as they can't see to fish," said Grahame Madge.
"Temperature wise it is probably ideal for them, but when you get these brown rivers they can't see to fish, I would suspect that some kingfishers would be facing a really hard time at present."
There have been some concerns that the massive amount of flooding now being seen across farmland may pick up and concentrate agricultural fertilisers, leading to a poisoning of the water and the land.
"The thing is that maybe smaller floods are worse for over-enrichment," said Tim Collins, from Natural England.
"What we are getting here is massive dilution, so it may be that the stuff that might have been deposited with smaller inundations may actually be dissolved and washed away - we simply can't tell yet."
There have also been suggestions from animal welfare campaigners that other species, including badgers, may be threatened by the duration of the floods.
They argue that animals that have been subjected to a pilot culling trial in Somerset may now be facing a more natural threat.
"Some setts will almost certainly have been damaged or flooded out completely, meaning that whole badger families could be disturbed," said Mark Jones from Humane Society International.
"There will be cubs in those setts right now and it's possible that some cubs will have drowned too."
The scale and extent of the impact of flooding on species like badgers has still to be determined.
According to Tim Collins from Natural England, flooding is part of the way that natural systems work and wildlife generally can cope.
"From an ecological perspective, mortality is a natural occurrence and not something we should be unduly disturbed about at a species level."
What is certain is that there has been plenty of damage being done to conservation infrastructure such as smashed up bird watching hides, footpaths washed away and visitor centres being flooded.
The Lincolnshire Wildlife Trust suffered badly as a result of the December surges, and are now looking at £1m insurance claim for damages to paths, hides and buildings.
"At Gibraltar Point which is one of our most popular nature reserves, we're not going to have a visitor centre there for a significant time because it needs complete rebuilding," said Rachel Shaw with the Trust.
"People can still go bird watching but it changes the whole nature of that place as a nature reserve."
It will take some time for the waters to recede, but it will take longer for a full assessment of the true cost of flooding on wildlife and the environment.
(Text taken from BBC website)

British Birds Journal February 2014 Issue: Best Bird Book List for 2013

The February 2014 issue of British Birds lists the BB / British Trust for Ornithology best bird books of the previous year. All books reviewed in British Birds, in BTO News and on the BTO website are eligible for the award.
The BB/BTO Best Bird Book of the Year 2013
Winner: Birds and People
By Mark Cocker, illustrated by David Tipling; Jonathan Cape, 2013.
Reviewed in BB by D. I. M. Wallace (Brit. Birds 106: 557–558).

2nd: The Warbler Guide
By Tom Stephenson and Scott Whittle; Princeton University Press, 2013.
Reviewed in BB by Peter Kennerley (Brit. Birds 106: 693–694).

3rd: The Unfeathered Bird
By Katrina van Grouw; Princeton University Press, 2013.
Reviewed in BB by David Parkin (Brit. Birds 106: 294–295).

4th: The World’s Rarest Birds
By Erik Hirschfeld, Andy Swash and Robert Still; Princeton University Press/WILDGuides, 2013.
Reviewed in BB by Paul Harvey (Brit. Birds 106: 355–356).

5th: Birds and habitat: relationships in changing landscapes
Edited by R. J. Fuller; Cambridge 2012.(BB review in press)

6th: Partridges
By G. R. Potts; Collins 2012.
Reviewed in BB by Ian Newton (Brit. Birds 106: 118–119).

High Recommended Titles
Return to One Man’s Island (by Keith Brockie, Birlinn, 2012 – see Brit. Birds 106: 48–49)  
The Long, Wild Shore – Bird and Seal Seasons on Blakeney Point (by James McCallum, Silver Brant, 2012 – see Brit. Birds 106: 174). 
The Crossley ID Guide: Raptors (by Richard Crossley, Jerry Liguori and Brian Sullivan, Princeton University Press, 2013 – see Brit. Birds 106: 753). 
The Mandarin Duck (by Christopher Lever, Poyser, 2012 – see Brit. Birds 106: 354–355) 
The Rutland Water Ospreys (by Tim Mackrill, Bloomsbury, 2013 – see Brit. Birds 106: 293–294). 
Birds in a Cage (by Derek Niemann, Short Books, 2012 – see Brit. Birds 106: 234). 
Handbook of the Birds of the World. Special Volume: New Species and Global Index (edited by Josep del Hoyo, Andrew Elliott, Jordi Sargatal and David A. Christie; Lynx Edicions, 2013 – seeBrit. Birds 106: 695). 
The Birds of Africa. Volume VIII: The Malagasy Region (by Frank Hawkins and Roger Safford; illustrated by John Gale and Brian Small; Christopher Helm, 2013 – BB review in prep.). 

Tuesday, 18 February 2014

Sparrowhawk (Accipiter nisus): close examination of fallen bird.

Never before have I had the opportunity to examine a Sparrowhawk (Accipiter nisus) in such detail after one was found dead in our local park. There were no obvious signs that it had been killed by illegal activity and so it must have been hit by a car or flew into a building or overhead cable.
Weighing approximately 160g I believe it to be a male; much smaller and lighter than I imagined after seeing one frequently fly through my garden - the same bird potentially. It will be sent to the Predatory Bird Monitoring Scheme where it can play its part in scientific research. As much as the investigative scientist in me wanted to dissect, label, catalog, and display this bird, I think this scheme will benefit more. They will send a full report on the bird to me after careful examination. I took a few photographs to remind me of this fantastic bird.