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Thursday, 26 February 2015

Oxidative Stress in Endurance Flight: A study of the European Robin. Jenni-Eiermann et al PLoS ONE May 2014

Oxidative Stress in Endurance Flight: An Unconsidered Factor in Bird Migration

Susanne Jenni-Eiermann (E-mail:

Swiss Ornithological Institute, Sempach, Switzerland
Lukas Jenni,
Swiss Ornithological Institute, Sempach, Switzerland
Shona Smith,
Institute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
David Costantini
Institute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom, Department of Biology, University of Antwerp, Wilrijk, Belgium

Jenni-Eiermann S, Jenni L, Smith S, Costantini D (2014) Oxidative Stress in Endurance Flight: An Unconsidered Factor in Bird Migration. PLoS ONE 9(5): e97650. doi:10.1371/journal.pone.0097650



Migrating birds perform extraordinary endurance flights, up to 200 h non-stop, at a very high metabolic rate and while fasting. Such an intense and prolonged physical activity is normally associated with an increased production of reactive oxygen and nitrogen species (RONS) and thus increased risk of oxidative stress. However, up to now it was unknown whether endurance flight evokes oxidative stress. We measured a marker of oxidative damage (protein carbonyls, PCs) and a marker of enzymatic antioxidant capacity (glutathione peroxidase, GPx) in the European robin (Erithacus rubecula), a nocturnal migrant, on its way to the non-breeding grounds. Both markers were significantly higher in European robins caught out of their nocturnal flight than in conspecifics caught during the day while resting. Independently of time of day, both markers showed higher concentrations in individuals with reduced flight muscles. Adults had higher GPx concentrations than first-year birds on their first migration. These results show for the first time that free-flying migrants experience oxidative stress during endurance flight and up-regulate one component of antioxidant capacity. We discuss that avoiding oxidative stress may be an overlooked factor shaping bird migration strategies, e.g. by disfavouring long non-stop flights and an extensive catabolism of the flight muscles.

Review Summary
Migratory birds have evolved specialised biochemical and cellular mechanisms, such as the method of lipid transport from adipose tissue direct to the mitochondria of the flight muscles. This allows them to manage the stresses of migratory flight that may include days of non-stop flying, whilst fasting, at a high metabolic rate. These high levels of catabolic processes are likely to generate quantities of reactive oxygen and nitrogen species (RONS) which should be harmful to the bird due to oxidative stress effects. The mechanism of oxidative balance in the Robin during migration across Europe is the subject of this paper.
The authors investigated a marker of oxidative damage and a marker of enzymatic antioxidant capacity in red blood cells of a migrant passerine, the European robin. These birds were caught out of migratory flight, towards the non-breeding grounds, at a Swiss Alpine Pass (Col de Bretolet located at the border between Switzerland and France) during the Autumn migration of 2011. They chose the European robin because it is the only nocturnal migrant which uses the Alpine pass for resting and feeding at day in noticeable numbers, and therefore they could compare markers of oxidative stress in two metabolic phases; the phase of extremely high metabolic rate during endurance exercise while fasting, and the phase of low metabolic rate during resting and foraging. 

Capture and Analysis
A total of 101 European robins were caught, 62 at night (44 first-year birds, 16 adults, 2 undetermined) and 39 during daylight or at dawn (29 first-years, 9 adults, 1 undetermined). 
Measurements of each bird were made as follows:

  1. Age
  2. Weight
  3. Third outermost primary feather length
  4. Subcutaneous fat score (The visible amount of subcutaneous fat deposits between the furcula and on the abdomen was scored on a scale ranging from 0 to 8; with 0 representing no visible fat.)
  5. Breast muscle score (0-3; with 0 leanest)
  6. Blood: protein carbonyls (PCs) - biomarker of oxidative damage
  7. Blood: activity of glutathione peroxidase (GPx) - biomarker of antioxidant activity
  8. Time of capture relative to dawn - negative values (i.e. before dawn) indicating captures at night and positive values indicating captures after dawn, during the day


Figure 1
Relationship between (a) protein carbonyls (PCs) (nmol/mg protein) of European robins and capture time since dawn, and (b) glutathione peroxidase (GPx) (U/l haemolysate) and capture time since dawn (N = 95).

Dawn is set to zero. Negative values (i.e. before dawn) indicate captures at night and positive values captures after dawn during the day. Dots are raw data points. The linear and cubic relationships with 95% confidence interval are derived from the models presented in Table 1 and given for muscle score 2 (PCs) and for young birds with muscle score 2 (GPx), respectively.

Figure 2
(a) Mean (95% confidence intervals) protein carbonyls (PCs) (nmol/mg protein) corrected for the linear relationship with time since dawn for muscle score 1 (N = 23), 2 (N = 63) and 3 (N = 9). For statistics see Table 1. (b) Mean (95% confidence intervals) glutathione peroxidase (GPx) (U/l haemolysate) corrected for the cubic relationship with time since dawn and age for muscle score 1 (N = 22), 2 (N = 64) and 3 (N = 9). (c) Mean (95% confidence intervals) glutathione peroxidase (U/l haemolysate) corrected for the cubic relationship with time since dawn and muscle for first-year (N = 70) and adult (N = 25) European robins.

Protein Carbonyl Levels - oxidative damage marker
The level of PCs was shown to reduce over time with the highest levels during the night and the lowest during the hours after dawn, however the confidence limits are quite large as there are fewer birds sampled at the upper and lower sampling times. 
Muscle score of 1 (lean birds) showed higher PC levels than those with muscle scores 2 and 3. Muscle score estimates the thickness of the breast muscle, representing breast muscle protein mass, and ranges from 0 to 3.
Neither fat score nor age had significant effects on PC level.

Glutathione Peroxidase Levels - antioxidant activity marker
The concentration of GPx in red blood cells was significantly dependent on time since dawn and on muscle score and age, but not fat score. It was high during the first part of the night, slightly lower in the middle part and peaked at dawn. After dawn GPx concentration decreased throughout the day in robins resting and feeding. 
The highest GPx concentrations were found in lean birds (muscle score 1), medium levels for muscle score 2, and the lowest levels for muscle score 3. Adults had significantly higher GPx concentrations than first-year birds.

Concluding Remarks
The study shows good evidence that this migratory bird, the European robin, is showing evidence of both oxidative stress and increase in a marker for the subsequent biochemical protection response. Migration journeys that cover significant distances over lengthy time-spans must therefore have measurable effects on a bird's fitness and therefore will partially determine the success or failure to meet breeding deadlines or areas of food supplies. It is crucial that the birds are fit and healthy with good muscle development to withstand the effects of the long flights undertaken. Understanding the costs versus benefits of oxidative stress response in migratory birds may be another tool, useful in research into avian migration studies.

Wednesday, 25 February 2015

What's new for 'birdRS' in PubMed. February 2015, Week 3

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
View complete results in PubMed (results may change over time).

PubMed Results

1. J Evol Biol. 2015 Feb 18. doi: 10.1111/jeb.12605. [Epub ahead of print]

Bird predation selects for wing shape and coloration in a damselfly.

Outomuro D1, Johansson F.
Author information:
Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.


Wing shape is related to flight performance, which is expected to be under selection for improving flight behaviours such as predator avoidance. Moreover, wing conspicuousness, usually involved in sexual selection processes, is also relevant in terms of predation risk. In this study, we examined how predation by a passerine bird, the white wagtail Motacilla alba, selects wing shape and wing colour patch size in males of the banded demoiselle Calopteryx splendens. The wing colour patch is intra- and intersexually selected in the study species. In a field study, we compared wings of live damselflies to wings of predated damselflies which are always discarded after predation. Based on aerodynamic theory and a previous study on wing shape of territorial tactics in damselflies, we predicted an overall short and broad wing, with a concave front margin shape to be selected by predation. This shape would be expected to improve escaping ability. Moreover, we predicted that wing patch size should be negatively selected by predation. We found that selection operated differently on fore- and hindwings. In contrast to our predictions, predation favoured a slender general forewing shape. However, the predicted wing shape was favoured in hindwings. We also found selection favouring a narrower wing colour patch. Our results suggest different roles of fore- and hindwings in flight, as previously suggested for Calopteryx damselflies and shown for butterflies and moths. Forewings would be more involved in sustained flight and hindwings in flight manoeuvrability. Our results differ somehow from a recently published work in the same study system, but using another population, suggesting that selection can fluctuate across space, despite the simplicity of this predator-prey system. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25693863 [PubMed - as supplied by publisher]

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2. Ecol Evol. 2015 Feb;5(3):781-98. doi: 10.1002/ece3.1400. Epub 2015 Jan 20.

Evolution of leaf warbler songs (Aves: Phylloscopidae).

Tietze DT1, Martens J2, Fischer BS3, Sun YH4, Klussmann-Kolb A5, Päckert M6.
Author information:
Institute of Ecology, Evolution and Diversity, Goethe University Max-von-Laue-Straße 13, 60439, Frankfurt am Main, Germany ; Institute of Pharmacy and Molecular Biotechnology, Heidelberg University Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
Institute of Zoology, Johannes Gutenberg University 55099, Mainz, Germany.
Institute of Ecology, Evolution and Diversity, Goethe University Max-von-Laue-Straße 13, 60439, Frankfurt am Main, Germany.
Key Laboratory of Animal Ecology and Conservation, Institute of Zoology, Chinese Academy of Sciences 100101, Beijing, China.
Institute of Ecology, Evolution and Diversity, Goethe University Max-von-Laue-Straße 13, 60439, Frankfurt am Main, Germany ; Zoologisches Forschungsmuseum Alexander Koenig Adenauerallee 160, 53113, Bonn, Germany.
Senckenberg Natural History Collections, Museum of Zoology Königsbrücker Landstraße 159, 01109, Dresden, Germany.


Songs in passerine birds are important for territory defense and mating. Speciation rates in oscine passerines are so high, due to cultural evolution, that this bird lineage makes up half of the extant bird species. Leaf warblers are a speciose Old-World passerine family of limited morphological differentiation, so that songs are even more important for species delimitation. We took 16 sonographic traits from song recordings of 80 leaf warbler taxa and correlated them with 15 potentially explanatory variables, pairwise, and in linear models. Based on a well-resolved molecular phylogeny of the same taxa, all pairwise correlations were corrected for relatedness with phylogenetically independent contrasts and phylogenetic generalized linear models were used. We found a phylogenetic signal for most song traits, but a strong one only for the duration of the longest and of the shortest element, which are presumably inherited instead of learned. Body size of a leaf warbler species is a constraint on song frequencies independent of phylogeny. At least in this study, habitat density had only marginal impact on song features, which even disappeared through phylogenetic correction. Maybe most leaf warblers avoid the deterioration through sound propagation in dense vegetation by singing from exposed perches. Latitudinal (and longitudinal) extension of the breeding ranges was correlated with most song features, especially verse duration (longer polewards and westwards) and complexity (lower polewards). Climate niche or expansion history might explain these correlations. The number of different element types per verse decreases with elevation, possibly due to fewer resources and congeneric species at higher elevations.
PMCID: PMC4328779 Free Article
PMID: 25691998 [PubMed]

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3. Ecol Evol. 2015 Feb;5(3):759-68. doi: 10.1002/ece3.1387. Epub 2015 Jan 17.

No species is an island: testing the effects of biotic interactions on models of avian niche occupation.

Morelli F1, Tryjanowski P2.
Author information:
Faculty of Biological Sciences, University of Zielona Gora Prof. Z. Szafrana St. 1, Zielona Gora, 65-516, Poland ; Faculty of Environmental Sciences, Department of Applied Geoinformatics and Spatial Planning, Czech University of Life Sciences Prague Kamýcká 129, Prague 6, 165 00, Czech Republic.
Institute of Zoology, Poznan University of Life Sciences Wojska Polskiego 71 C, Poznań, 60-625, Poland.


Traditionally, the niche of a species is described as a hypothetical 3D space, constituted by well-known biotic interactions (e.g. predation, competition, trophic relationships, resource-consumer interactions, etc.) and various abiotic environmental factors. Species distribution models (SDMs), also called "niche models" and often used to predict wildlife distribution at landscape scale, are typically constructed using abiotic factors with biotic interactions generally been ignored. Here, we compared the goodness of fit of SDMs for red-backed shrike Lanius collurio in farmlands of Western Poland, using both the classical approach (modeled only on environmental variables) and the approach which included also other potentially associated bird species. The potential associations among species were derived from the relevant ecological literature and by a correlation matrix of occurrences. Our findings highlight the importance of including heterospecific interactions in improving our understanding of niche occupation for bird species. We suggest that suite of measures currently used to quantify realized species niches could be improved by also considering the occurrence of certain associated species. Then, an hypothetical "species 1" can use the occurrence of a successfully established individual of "species 2" as indicator or "trace" of the location of available suitable habitat to breed. We hypothesize this kind of biotic interaction as the "heterospecific trace effect" (HTE): an interaction based on the availability and use of "public information" provided by individuals from different species. Finally, we discuss about the incomes of biotic interactions for enhancing the predictive capacities on species distribution models.
PMCID: PMC4328777 Free Article
PMID: 25691996 [PubMed]

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4. Ecol Evol. 2015 Jan;5(2):450-8. doi: 10.1002/ece3.1355. Epub 2015 Jan 2.

All you can eat: is food supply unlimited in a colonially breeding bird?

Hoi H1, Krištofík J2, Darolová A2.
Author information:
Department of Integrative Biology and Evolution, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Austria.
Institute of Zoology, Slovak Academy of Sciences Bratislava, Slovakia.


Food availability is generally considered to determine breeding site selection and therefore plays an important role in hypotheses explaining the evolution of colony formation. Hypotheses trying to explain why birds join a colony usually assume that food is not limited, whereas those explaining variation in colony size suggest that food is under constraint. In this study, we investigate the composition and amount of food items not eaten by the nestlings and found in nest burrows of colonially nesting European bee-eaters (Merops apiaster). We aimed to determine whether this unconsumed food is an indicator of unlimited food supply, the result of mistakes during food transfer between parents and chicks or foraging selectivity of chicks. Therefore, we investigated the amount of dropped food for each nest in relation to reproductive performance and parameters reflecting parental quality. Our data suggest that parents carry more food to the nest than chicks can eat and, hence, food is not limited. This assumption is supported by the facts that there is a positive relationship between dropped food found in a nest and the number of fledglings, nestling age, and chick health condition and that the amount of dropped food is independent of colony size. There is variation in the amount of dropped food within colonies, suggesting that parent foraging efficiency may also be an important determinant. Pairs nesting in the center of a colony performed better than those nesting on the edge, which supports the assumption that quality differences between parents are important as well. However, dropped food cannot be used as an indicator of local food availability as (1) within-colony variation in dropped food is larger than between colony variation and, (2) the average amount of dropped food is not related to colony size.
PMCID: PMC4314275 Free Article
PMID: 25691970 [PubMed]

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5. Ecol Evol. 2015 Jan;5(2):345-56. doi: 10.1002/ece3.1345. Epub 2014 Dec 24.

Rainfall during parental care reduces reproductive and survival components of fitness in a passerine bird.

Öberg M1, Arlt D1, Pärt T1, Laugen AT2, Eggers S1, Low M1.
Author information:
Department of Ecology, Swedish University of Agricultural Sciences Box 7044, Uppsala, 75007, Sweden.
Department of Ecology, Swedish University of Agricultural Sciences Box 7044, Uppsala, 75007, Sweden ; Aronia Coastal Zone Research Team, Novia University of Applied Sciences & Åbo Academy University Raseborgsvägen 9, Ekenäs, 10600, Finland.


Adverse weather conditions during parental care may have direct consequences for offspring production, but longer-term effects on juvenile and parental survival are less well known. We used long-term data on reproductive output, recruitment, and parental survival in northern wheatears (Oenanthe oenanthe) to investigate the effects of rainfall during parental care on fledging success, recruitment success (juvenile survival), and parental survival, and how these effects related to nestling age, breeding time, habitat quality, and parental nest visitation rates. While accounting for effects of temperature, fledging success was negatively related to rainfall (days > 10 mm) in the second half of the nestling period, with the magnitude of this effect being greater for breeding attempts early in the season. Recruitment success was, however, more sensitive to the number of rain days in the first half of the nestling period. Rainfall effects on parental survival differed between the sexes; males were more sensitive to rain during the nestling period than females. We demonstrate a probable mechanism driving the rainfall effects on reproductive output: Parental nest visitation rates decline with increasing amounts of daily rainfall, with this effect becoming stronger after consecutive rain days. Our study shows that rain during the nestling stage not only relates to fledging success but also has longer-term effects on recruitment and subsequent parental survival. Thus, if we want to understand or predict population responses to future climate change, we need to consider the potential impacts of changing rainfall patterns in addition to temperature, and how these will affect target species' vital rates.
PMCID: PMC4314267 Free Article
PMID: 25691962 [PubMed]

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6. Evolution. 2015 Feb 17. doi: 10.1111/evo.12625. [Epub ahead of print]

Hatching asynchrony aggravates inbreeding depression in a songbird (Serinus canaria): An inbreeding-environment interaction.

de Boer RA1, Eens M, Fransen E, Müller W.
Author information:
Faculty of Science - Ethology - University of Antwerp, Universiteitsplein 1 - Campus Drie Eiken C1.25, B-2610, Wilrijk, Belgium.


Understanding how the intensity of inbreeding depression is influenced by stressful environmental conditions is an important area of enquiry in various fields of biology. In birds, environmental stress during early development is often related to hatching asynchrony; differences in age, and thus size, impose a gradient in conditions ranging from benign (first hatched chick) to harsh (last hatched chick). Here, we compared the effect of hatching order on growth rate in inbred (parents are full siblings) and outbred (parents are unrelated) canary chicks (Serinus canaria). We found that inbreeding depression was more severe under more stressful conditions, being most evident in later hatched chicks. Thus, consideration of inbreeding-environment interactions is of vital importance for our understanding of the biological significance of inbreeding depression and hatching asynchrony. The latter is particularly relevant given that hatching asynchrony is a widespread phenomenon, occurring in many bird species. The exact causes of the observed inbreeding-environment interaction are as yet unknown, but may be related to a decrease in maternal investment in egg contents with laying position (i.e. pre-hatching environment), or to performance of the chicks during sibling competition and/or their resilience to food shortage (i.e. post-hatching environment). This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25689753 [PubMed - as supplied by publisher]

7. Med Vet Entomol. 2015 Feb 16. doi: 10.1111/mve.12108. [Epub ahead of print]

Host preferences of ornithophilic biting midges of the genus Culicoides in the Eastern Balkans.

Bobeva A1, Zehtindjiev P, Ilieva M, Dimitrov D, Mathis A, Bensch S.
Author information:
Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria.


Many biting midges of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are competent vectors of a diverse number of pathogens. The identification of their feeding behaviour and of vector-host associations is essential for understanding their transmission capacity. By applying two different nested polymerase chain reaction (PCR) assays, of which one targeted the avian cyt b gene and the other targeted the COI gene of a wide range of vertebrates, we identified the blood hosts of six biting midge species including Culicoides circumscriptus, Culicoides festivipennis, Culicoides punctatus, Culicoides pictipennis, Culicoides alazanicus and Culicoides cf. griseidorsum, the latter two of which are reported in Bulgaria for the first time. Bird DNA was found in 50.6% of 95 investigated bloodmeals, whereas mammalian DNA was identified in 13.7%. Two Culicoides species were found to feed on both birds and mammals. There was remarkable diversity in the range of avian hosts: 23 species from four orders were identified in the abdomens of four Culicoides species. The most common bird species identified was the magpie, Pica pica (n = 7), which was registered in all four ornithophilic biting midge species. Six bloodmeals from the great tit, Parus major, were recorded only in C. alazanicus. None of the studied species of Culicoides appeared to be restricted to a single avian host.
© 2015 The Royal Entomological Society.
PMID: 25689114 [PubMed - as supplied by publisher]

8. Glob Chang Biol. 2015 Feb 16. doi: 10.1111/gcb.12862. [Epub ahead of print]

Vocal traits and diet explain avian sensitivities to anthropogenic noise.

Francis CD1.
Author information:
National Evolutionary Synthesis Center, Durham, NC, 27705, USA; Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA.


Global population growth has caused extensive human-induced environmental change, including a near-ubiquitous transformation of the acoustical environment due to the propagation of anthropogenic noise. Because the acoustical environment is a critical ecological dimension for countless species to obtain, interpret and respond to environmental cues, highly novel environmental acoustics have the potential to negatively impact organisms that use acoustics for a variety of functions, such as communication and predator/prey detection. Using a comparative approach with 308 populations of 183 bird species from 14 locations in Europe, North American and the Caribbean, I sought to reveal the intrinsic and extrinsic factors responsible for avian sensitivities to anthropogenic noise as measured by their habitat use in noisy versus adjacent quiet locations. Birds across all locations tended to avoid noisy areas, but trait-specific differences emerged. Vocal frequency, diet and foraging location predicted patterns of habitat use in response to anthropogenic noise, but body size, nest placement and type, other vocal features and the type of anthropogenic noise (chronic industrial vs. intermittent urban/traffic noise) failed to explain variation in habitat use. Strongly supported models also indicated the relationship between sensitivity to noise and predictive traits had little to no phylogenetic structure. In general, traits associated with hearing were strong predictors - species with low-frequency vocalizations, which experience greater spectral overlap with low-frequency anthropogenic noise tend to avoid noisy areas, whereas species with higher frequency vocalizations respond less severely. Additionally, omnivorous species and those with animal-based diets were more sensitive to noise than birds with plant-based diets, likely because noise may interfere with the use of audition in multimodal prey detection. Collectively, these results suggest that anthropogenic noise is a powerful sensory pollutant that can filter avian communities nonrandomly by interfering with birds' abilities to receive, respond to and dispatch acoustic cues and signals.
© 2015 John Wiley & Sons Ltd.
PMID: 25688983 [PubMed - as supplied by publisher]

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9. Oecologia. 2015 Feb 18. [Epub ahead of print]

Changes in the apparent survival of a tropical bird in response to the El Niño Southern Oscillation in mature and young forest in Costa Rica.

Wolfe JD1, Ralph CJ, Elizondo P.
Author information:
USDA Forest Service, Pacific Southwest Research Station, Arcata, USA,


The effects of habitat alteration and climatic instability have resulted in the loss of bird populations throughout the globe. Tropical birds in particular may be sensitive to climate and habitat change because of their niche specialization, often sedentary nature, and unique life-cycle phenologies. Despite the potential influence of habitat and climatic interactions on tropical birds, we lack comparisons of avian demographics from variably aged forests subject to different climatic phenomena. Here, we measured relationships between forest type and climatic perturbations on White-collared Manakin (Manacus candei), a frugivorous tropical bird, by using 12 years of capture data in young and mature forests in northeastern Costa Rica. We used Cormack-Jolly-Seber models and an analysis of deviance to contrast the influence of the El Niño Southern Oscillation (ENSO) on manakin survival. We found that ENSO had little effect on manakin survival in mature forests. Conversely, in young forests, ENSO explained 79 % of the variation where dry El Niño events negatively influenced manikin survival. We believe mature forest mitigated negative effects of dry El Niño periods and can serve as refugia for some species by buffering birds from climatic instability. Our results represent the first published documentation that ENSO influences the survival of a resident Neotropic landbird.
PMID: 25687831 [PubMed - as supplied by publisher]

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10. Gigascience. 2014 Dec 11;3(1):32. doi: 10.1186/2047-217X-3-32. eCollection 2014.

The birds of Genome10K.

Author information:
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004 Russia ; Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004 USA.
Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064 USA.
San Diego Zoo Institute for Conservation Research, Escondido, CA 92027 USA.


Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers - both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science, Genome Biology and GigaScience (which also included pre-publication data release). These present the successful beginnings of an international interdisciplinary venture, the Avian Phylogenomics Project that lets us view, through a genomics lens, modern bird species and the evolutionary events that produced them.
PMCID: PMC4326320 Free PMC Article
PMID: 25685332 [PubMed]

11. Methods Ecol Evol. 2015 Jan 1;6(1):109-118.

Decomposing changes in phylogenetic and functional diversity over space and time.

Chalmandrier L1, Münkemüller T1, Devictor V2, Lavergne S1, Thuiller W1.
Author information:
Univ. Grenoble Alpes, LECA, F-38000 Grenoble, France ; CNRS, LECA, F-38000 Grenoble, France.
Institut des Sciences de l'Évolution de Montpellier, UMR CNRS 5554, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.


The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial β-diversities and their interaction.We characterised the range of β-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial β-diversities are independent from each other and from α and γ-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial β-diversities lacked such properties.We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys.
PMCID: PMC4326675 Free PMC Article
PMID: 25685310 [PubMed]

12. Mol Phylogenet Evol. 2015 Feb 12. pii: S1055-7903(15)00032-9. doi: 10.1016/j.ympev.2015.02.004. [Epub ahead of print]

Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae).

Rocha TC1, Sequeira F2, Aleixo A3, Rêgo PS4, Sampaio I4, Schneider H4, Vallinoto M5.
Author information:
Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, PA 68600-000, Brazil.
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.
Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Caixa Postal 399, Belém, PA 66077 530, Brazil.
Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, PA 68600-000, Brazil.
Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, PA 68600-000, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão 4485-661, Portugal. Electronic address:


The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus/susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (β-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear β-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus/susurrans complex: X. susurrans, X. guttatus, and X. guttatoides.
Copyright © 2015 Elsevier Inc. All rights reserved.
PMID: 25683049 [PubMed - as supplied by publisher]

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13. Ticks Tick Borne Dis. 2015 Feb 11. pii: S1877-959X(15)00017-5. doi: 10.1016/j.ttbdis.2015.01.004. [Epub ahead of print]

Molecular identification of Ehrlichia species and host bloodmeal source in Amblyomma americanum L. from two locations in Tennessee, United States.

Harmon JR1, Scott MC2, Baker EM2, Jones CJ3, Hickling GJ2.
Author information:
University of Tennessee Institute of Agriculture, Entomology and Plant Pathology Department, United States; University of Tennessee Institute of Agriculture, Center for Wildlife Health, United States. Electronic address:
University of Tennessee Institute of Agriculture, Center for Wildlife Health, United States.
University of Tennessee Institute of Agriculture, Entomology and Plant Pathology Department, United States.


The current status of tick-borne diseases in the southeastern United States is challenging to define due to emerging pathogens, uncertain tick/host relationships, and changing disease case definitions. A golf-oriented retirement community on the Cumberland Plateau in Tennessee experienced an ehrlichiosis outbreak in 1993, prompting efforts to reduce the local tick population using '4-Poster' acaricide devices targeting white-tailed deer (Odocoileus virginianus). In 2009, the prevalence of Ehrlichia spp. in questing ticks was surveyed in the area and compared to a Tennessee state park where acaricide had not been applied. The range of wildlife hosts that immature Amblyomma americanum fed upon and the role that these hosts may play in pathogen dynamics were investigated using a reverse line blot (RLB) bloodmeal analysis technique. Amblyomma americanum was by far the most common tick species in both study areas (>99% of ticks collected). Of 303 adult and nymphal A. americanum tested at the retirement community, six were positive for Ehrlichia chaffeensis (2.0%), 16 were positive for E. ewingii (5.3%), and six were positive for Panola Mountain Ehrlichia (2.0%). This is the first confirmation of Panola Mountain Ehrlichia in A. americanum from the state of Tennessee. The 9.3% prevalence of Ehrlichia spp. in ticks from the retirement community was similar to that detected at the state park site (5.5%), suggesting that the 4-Poster treatment had not been sufficient to reduce Ehrlichia spp. cycling in the tick population. At both study sites, A. americanum fed on a wide range of mammal and bird species, with a minority of detectable bloodmeals coming from deer. Of the Ehrlichia-infected nymphs with positive bloodmeal identification, none fed on deer, indicating that multiple vertebrate species are contributing to sylvatic maintenance of Ehrlichia spp. at these sites. This highlights the difficulty of attempting to reduce the risk of tick-borne disease through host-targeted interventions alone.
Copyright © 2015 Elsevier GmbH. All rights reserved.
PMID: 25682494 [PubMed - as supplied by publisher]

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14. Poult Sci. 2015 Feb 12. pii: pev021. [Epub ahead of print]

Welfare and performance in layers following temporary exclusion from the litter area on introduction to the layer facility.

Alm M1, Wall H2, Holm L3, Wichman A4, Palme R5, Tauson R2.
Author information:
Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-750 07 Uppsala, Sweden
Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-750 07 Uppsala, Sweden.
Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, SE-750 07 Uppsala, Sweden.
Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 7068, SE-750 07 Uppsala, Sweden.
Department of Biomedical Sciences/Unit of Physiology, Pathophysiology, and Experimental Endocrinology, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria.


When introduced to the laying facility, pullets are sometimes temporarily excluded from the litter area in order to help them locate food and water, and to prevent floor-laid eggs. This procedure is not permitted in Sweden, because it involves denying access to both litter and space, which may have a negative effect on bird welfare. The present study investigated how the welfare and performance of layers were affected by this temporary exclusion on introduction of hens to the laying facility. The study included 600 floor-reared Dekalb White layers obtained at 16 wk age and housed in 6 groups of 100 in a conventional single-tier floor-laying system. Birds were either given full access to the litter area during the whole study or were excluded from the litter area during the first 2 wk after transfer to the laying facility. From 18 to 72 wk age, birds in both treatments had full access to the litter area. Excluding birds from the litter area for 2 wk resulted in better feather cover and reduced fearfulness, according to novel object and tonic immobility tests. Furthermore, birds initially excluded from the litter area produced eggs with a lower proportion of shell irregularities than birds with full access to the litter area throughout. No difference was found in corticosterone metabolites in droppings rate of lay, mortality, or proportion of floor-laid eggs. In conclusion, none of the parameters studied indicated that the welfare of laying hens was compromised by temporary exclusion from the litter area on introduction to the laying facility. In fact, some of the data suggested that bird welfare had improved.
© 2015 Poultry Science Association Inc.
PMID: 25681475 [PubMed - as supplied by publisher]

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Wednesday, 18 February 2015

What's new for 'birdRS' in PubMed: February 2015, Week 2

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PubMed Results

1. PLoS One. 2015 Feb 13;10(2):e0117071. doi: 10.1371/journal.pone.0117071.

Temporal Trends in Metal Pollution: Using Bird Excrement as Indicator.

Berglund ÅM1, Rainio MJ1, Eeva T1.
Author information:
Section of Ecology, University of Turku, Turku, Finland.


Past mining and smelting activities have resulted in metal polluted environments all over the world, but long-term monitoring data is often scarce, especially in higher trophic levels. In this study we used bird (Parus major and Ficedula hypoleuca) excrement to monitor metal pollution in the terrestrial environment following 16 years of continuously reduced emissions from a copper/nickel smelter in Finland. In the early 1990s, lead and cadmium concentrations dropped significantly in excrement, but the reduction did not directly reflect the changes in atmospheric emission from the smelter. This is likely due to a continuous contribution of metals also from the soil pool. We conclude that bird excrement can be used to assess changes in the environment as a whole but not specifically changes in atmospheric emission. Inter-annual variation in excrement concentration of especially copper and nickel demonstrates the importance of long-term monitoring to discern significant trends.
PMID: 25680108 [PubMed - as supplied by publisher]

2. Plant Biol (Stuttg). 2015 Feb 11. doi: 10.1111/plb.12312. [Epub ahead of print]

Pollination ecology of two species of Elleanthus (Orchidaceae): novel mechanisms and underlying adaptations to hummingbird pollination.

Nunes CE1, Amorim FW, Mayer JL, Sazima M.
Author information:
Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.


Relationships among floral biology, floral micromorphology and pollinator behaviour in bird-pollinated orchids are important issues to understand the evolution of the huge flower diversity within Orchidaceae. We aimed to investigate floral mechanisms underlying the interaction with pollinators in two hummingbird-pollinated orchids occurring in the Atlantic forest. We assessed floral biology, nectar traits, nectary and column micromorphologies, breeding systems and pollinators. In both species, nectar is secreted by lip calli through spaces between the medial lamellar surfaces of epidermal cells. Such form of floral nectar secretion has not been previously described. Both species present functional protandry and are self-compatible yet pollinator-dependent. Fruit sets in hand-pollination experiments were more than twice those under natural conditions, evidencing pollen limitation. The absence of fruit set in interspecific crosses suggests the existence of post-pollination barriers between these synchronopatric species. In Elleanthus brasiliensis, fruits resulting from cross-pollination and natural conditions were heavier than those resulting from self-pollination, suggesting advantages to cross-pollination. Hummingbirds pollinated both species, which share at least one pollinator species. Species differences in floral morphologies led to distinct pollination mechanisms. In E. brasiliensis, attachment of pollinaria to the hummingbird bill occurs through a lever apparatus formed by an appendage in the column, another novelty to the knowledge of orchids. In E. crinipes, pollinaria attachment occurs by simple contact with the bill during insertion into the flower tube, which fits tightly around the bill. The novelties described here illustrate the overlooked richness in ecology and morphophysiology in Orchidaceae. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25678071 [PubMed - as supplied by publisher]

3. Br Poult Sci. 2015 Feb 13. [Epub ahead of print]

The reproductive response of female ostriches to dietary protein.

Brand TS1, Olivier TR, Gous RM.
Author information:
1 Institute for Animal Production: Elsenburg , Western Cape Department of Agriculture , Private Bag X1, Elsenburg , 7607 , South Africa.


1. A study was conducted with breeding ostriches over two consecutive breeding seasons to determine their response to different concentrations of a well-balanced dietary protein. 2. Five concentrations of protein were fed to both females and males at an intake of 2.5 kg/bird d. The respective diets contained 75, 91, 108, 123 and 140 g protein/kg feed with energy held constant at 9.2 MJ metabolisable energy/kg feed. 3. Egg production (mean ± SE, 39.1 ± 3.6 eggs/female/season) was unaffected by dietary protein concentration. Similarly, no significant trends were found for the number of unfertilised eggs (9.1 ± 1.8), dead-in-shell chicks (8.2 ± 1.3), the number of chicks hatched (19.5 ± 2.5) and change in the mass of females (-16.3 ± 10.2 kg). Egg weight decreased linearly as dietary protein content increased. 4. Age of the ostrich female had a highly significant effect on the number of eggs laid, the number of chicks hatched, the number of dead-in-shell and infertile eggs produced per hen, as well as the mass change of female breeding birds, but did not affect the response of any of these variables to dietary protein content. 5. It was concluded that ostriches do not benefit from dietary protein contents greater than about 75 g/kg when this is fed at a daily total feed intake rate of 2.5 kg/bird during the breeding season.
PMID: 25677946 [PubMed - as supplied by publisher]

4. Mol Ecol. 2015 Feb 9. doi: 10.1111/mec.13105. [Epub ahead of print]

Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network.

Husemann M1, Cousseau L, Callens T, Matthysen E, Vangestel C, Hallmann C, Lens L.
Author information:
General Zoology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.


The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analyzed the demography and genetic population structure over a recent fifteen year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modeling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behavior helps to buffer such effects. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25677704 [PubMed - as supplied by publisher]

5. Am Nat. 2015 Mar;185(3):390-405. doi: 10.1086/679613. Epub 2015 Jan 22.

The Level of an Intracellular Antioxidant during Development Determines the Adult Phenotype in a Bird Species: A Potential Organizer Role for Glutathione.

Romero-Haro AA1, Alonso-Alvarez C.
Author information:
Instituto de Investigación en Recursos Cinegéticos, Consejo Superior de Investigaciones Científicas, Universidad de Castilla-La Mancha, Junta de Comunidades de Castilla-La Mancha, Ronda de Toledo s/n, 13071 Ciudad Real, Spain.


Abstract Life-history traits are often involved in trade-offs whose outcome would depend on the availability of resources but also on the state of specific molecular signals. Early conditions can influence trade-offs and program the phenotype throughout the lifetime, with oxidative stress likely involved in many taxa. Here we address the potential regulatory role of a single intracellular antioxidant in life-history trade-offs. Blood glutathione levels were reduced in a large sample of birds (zebra finch Taeniopygia guttata) during development using the synthesis inhibitor buthionine sulfoximine (BSO). Results revealed several modifications in the adult phenotype. BSO-treated nestlings showed lower glutathione and plasma antioxidant levels. In adulthood, BSO birds endured greater oxidative damage in erythrocytes but stronger expression of a sexual signal. Moreover, adult BSO females also showed weaker resistance to oxidative stress but were heavier and showed better body condition. Results suggest that low glutathione values during growth favor the investment in traits that should improve fitness returns, probably in the form of early reproduction. Higher oxidative stress in adulthood may be endured if this cost is paid later in life. Either the presence of specific signaling mechanisms or the indirect effect of increased oxidative stress can explain our findings.
PMID: 25674693 [PubMed - in process]

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6. Am Nat. 2015 Mar;185(3):380-9. doi: 10.1086/679612. Epub 2015 Jan 22.

Postnatal Growth Rates Covary Weakly with Embryonic Development Rates and Do Not Explain Adult Mortality Probability among Songbirds on Four Continents.

Martin TE1, Oteyza JC, Mitchell AE, Potticary AL, Lloyd P.
Author information:
US Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Missoula, Montana 59812.


Abstract Growth and development rates may result from genetic programming of intrinsic processes that yield correlated rates between life stages. These intrinsic rates are thought to affect adult mortality probability and longevity. However, if proximate extrinsic factors (e.g., temperature, food) influence development rates differently between stages and yield low covariance between stages, then development rates may not explain adult mortality probability. We examined these issues based on study of 90 songbird species on four continents to capture the diverse life-history strategies observed across geographic space. The length of the embryonic period explained little variation (ca. 13%) in nestling periods and growth rates among species. This low covariance suggests that the relative importance of intrinsic and extrinsic influences on growth and development rates differs between stages. Consequently, nestling period durations and nestling growth rates were not related to annual adult mortality probability among diverse songbird species within or among sites. The absence of a clear effect of faster growth on adult mortality when examined in an evolutionary framework across species may indicate that species that evolve faster growth also evolve physiological mechanisms for ameliorating costs on adult mortality. Instead, adult mortality rates of species in the wild may be determined more strongly by extrinsic environmental causes.
PMID: 25674692 [PubMed - in process]

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7. Proc Biol Sci. 2015 Mar 22;282(1803). pii: 20142523. doi: 10.1098/rspb.2014.2523.

Experimental food supplementation reveals habitat-dependent male reproductive investment in a migratory bird.

Kaiser SA1, Sillett TS2, Risk BB3, Webster MS4.
Author information:
Cornell Lab of Ornithology, and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20013, USA.
Department of Statistical Science, Cornell University, Ithaca, NY 14853, USA.
Cornell Lab of Ornithology, and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA.


Environmental factors can shape reproductive investment strategies and influence the variance in male mating success. Environmental effects on extrapair paternity have traditionally been ascribed to aspects of the social environment, such as breeding density and synchrony. However, social factors are often confounded with habitat quality and are challenging to disentangle. We used both natural variation in habitat quality and a food supplementation experiment to separate the effects of food availability-one key aspect of habitat quality-on extrapair paternity (EPP) and reproductive success in the black-throated blue warbler, Setophaga caerulescens. High natural food availability was associated with higher within-pair paternity (WPP) and fledging two broods late in the breeding season, but lower EPP. Food-supplemented males had higher WPP leading to higher reproductive success relative to controls, and when in low-quality habitat, food-supplemented males were more likely to fledge two broods but less likely to gain EPP. Our results demonstrate that food availability affects trade-offs in reproductive activities. When food constraints are reduced, males invest in WPP at the expense of EPP. These findings imply that environmental change could alter how individuals allocate their resources and affect the selective environment that drives variation in male mating success.
© 2015 The Author(s) Published by the Royal Society. All rights reserved.
PMID: 25673677 [PubMed - in process]

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8. Gigascience. 2014 Dec 11;3(1):26. doi: 10.1186/2047-217X-3-26. eCollection 2014.

Comparative genomic data of the Avian Phylogenomics Project.

Zhang G1, Li B2, Li C3, Gilbert MT4, Jarvis ED5, Wang J6; Avian Genome Consortium.
Author information:
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark ; Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102 Australia.
Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710 USA.
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark ; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China ; Department of Medicine, University of Hong Kong, Hong Kong, China.



The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics.


The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses.


Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.
PMCID: PMC4322804 Free PMC Article
PMID: 25671091 [PubMed]

9. PLoS One. 2015 Feb 10;10(2):e0117920. doi: 10.1371/journal.pone.0117920. eCollection 2015.

Yet another empty forest: considering the conservation value of a recently established tropical nature reserve.

Sreekar R1, Zhang K2, Xu J3, Harrison RD3.
Author information:
Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China; University of the Chinese Academy of Sciences, Beijing, China.
Ecology, Conservation, and Environment Center (ECEC), State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; University of the Chinese Academy of Sciences, Beijing, China.
Key Laboratory for Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China; World Agroforestry Centre, East Asia Node, Heilongtan, Kunming, Yunnan, China.


The primary approach used to conserve tropical biodiversity is in the establishment of protected areas. However, many tropical nature reserves are performing poorly and interventions in the broader landscape may be essential for conserving biodiversity both within reserves and at large. Between October 2010 and 2012, we conducted bird surveys in and around a recently established nature reserve in Xishuangbanna, China. We constructed a checklist of observed species, previously recorded species, and species inferred to have occurred in the area from their distributions and habitat requirements. In addition, we assessed variation in community composition and habitat specificity at a landscape-scale. Despite the fact that the landscape supports a large area of natural forest habitat (~50,000 ha), we estimate that >40% of the bird fauna has been extirpated and abundant evidence suggests hunting is the primary cause. A large proportion (52%) of the bigger birds (>20 cm) were extirpated and for large birds there was a U-shaped relationship between habitat breadth and extirpation probability. Habitat specificity was low and bird communities were dominated by widespread species of limited conservation concern. We question whether extending tropical protected area networks will deliver desired conservation gains, unless much greater effort is channeled into addressing the hunting problem both within existing protected areas and in the broader landscape.
Free Article
PMID: 25668338 [PubMed - in process]

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10. Sci Total Environ. 2015 Feb 6;514C:77-82. doi: 10.1016/j.scitotenv.2015.01.095. [Epub ahead of print]

Accumulation of Dechlorane Plus flame retardant in terrestrial passerines from a nature reserve in South China: The influences of biological and chemical variables.

Peng Y1, Wu JP2, Tao L1, Mo L3, Zheng XB1, Tang B1, Luo XJ4, Mai BX4.
Author information:
State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China. Electronic address:
Hainan Research Academy of Environmental Sciences, Haikou 571126, China.
State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.


Although a number of studies have addressed the bioaccumulation of Dechlorane Plus (DP) flame retardant in wildlife, few data are available on terrestrial organisms. This study examined the presence of DP isomers in the muscle tissue of seven terrestrial resident passerine species, i.e., the great tit (Parus major), the oriental magpie-robin (Copsychus saularis), the red-whiskered bulbul (Pycnonotus jocosus), the light-vented bulbul (Pycnonotus sinensis), the streak-breasted scimitar babbler (Pomatorhinus ruficollis), the long-tailed shrike (Lanius schach), and the orange-headed thrush (Zoothera citrina), from a national nature reserve located in South China. The ∑DP (sum of syn-DP and anti-DP) concentrations ranged from 1.2 to 104ng/g lipid weight, with significantly higher levels in insectivorous birds than in omnivorous birds. The overall exposure to DP isomers of the current passerines may be attributed to the intensive release of this pollutant from electronic waste recycling sites and industrial zones in the vicinity of the nature reserve. Species-specific DP isomeric profiles were also found, with significantly greater fanti values (the isomer fractions of anti-DP) in the red-whiskered bulbul and the oriental magpie-robin. Additionally, the fanti values were significantly negatively correlated to ∑DP concentrations for the individual bird samples, suggesting the influence of DP concentrations on the isomeric profiles.
Copyright © 2015. Published by Elsevier B.V.
PMID: 25666277 [PubMed - as supplied by publisher]

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11. J Evol Biol. 2015 Feb 9. doi: 10.1111/jeb.12595. [Epub ahead of print]

Visual modelling suggests a weak relationship between the evolution of ultraviolet vision and plumage colouration in birds.

Lind O1, Delhey K.
Author information:
Department of Philosophy, Lund University; Department of optometry and Vision Science, The University of Auckland.


Birds have sophisticated colour vision mediated by four cones types that cover a wide visual spectrum including ultraviolet (UV) wavelengths. Many birds have modest UV-sensitivity provided by violet-sensitive (VS) cones with sensitivity maxima between 400-425 nm. However, some birds have evolved higher UV-sensitivity and a larger visual spectrum given by UV-sensitive (UVS) cones maximally sensitive at 360-370 nm. The reasons for VS-UVS transitions and their relationship to visual ecology remain unclear. It has been hypothesized that the evolution of UVS-cone vision is linked to plumage colours so that visual sensitivity and feather colouration are "matched". This leads to the specific prediction that UVS-cone vision enhance the discrimination of plumage colours of UVS-birds while such an advantage is absent or less pronounced for VS-bird colouration. We test this hypothesis using knowledge of the complex distribution of UVS-cones among birds combined with mathematical modelling of colour discrimination during different viewing conditions. We find no support for the hypothesis, which, combined with previous studies suggests only a weak relationship between UVS-cone vision and plumage colour evolution. Instead we suggest that UVS-cone vision generally favours colour discrimination, which creates a non-specific selection pressure for the evolution of UVS-cones. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25664902 [PubMed - as supplied by publisher]
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12. Environ Toxicol Chem. 2015 Feb 7. doi: 10.1002/etc.2925. [Epub ahead of print]

Adverse effects of thiram treated seed ingestion on the reproductive performance and the offspring immune function of the red-legged partridge.

Lopez-Antia A1, Ortiz-Santaliestra ME, García-De Blas E, Camarero PR, Mougeot F, Mateo R.
Author information:
Institute of Research in Game Resources (IREC) CSIC-UCLM-JCCM, Ciudad Real, Spain.


Pesticide research has traditionally focused on compounds with high acute toxicity and/or persistence, but the adverse sublethal effects of pesticides with different properties may also have important consequences on exposed wildlife. The authors studied the effects of thiram, a fungicide used for seed coating with known effects as endocrine disruptor. Red-legged partridges (Alectoris rufa) (n=16 pairs/treatment group) were feeding wheat treated with 0%, 20% or 100% of the thiram application rate used in autumn (25 days) and late winter (10 days) mimicking cereal sowing periods. The authors studied the effects on reproductive performance, carotenoid-based ornamentation and cellular immune responsiveness of adult partridges, and their relationship with changes in oxidative stress biomarkers and plasma biochemistry. The authors also studied the effect of parental exposure on egg antioxidant content and on the survival, growth and cellular immune response of offspring. Exposure to thiram coated seeds delayed egg laying, reduced clutch size, and affected egg size and eggshell thickness. Partridges exposed to 20% thiram dose exhibited reduced egg fertility and brood size (55% and 28% of controls, respectively). Chick survival was unaffected by parental exposure to treated seeds, but adverse effects on their growth rate and cellular immune response were apparent. These effects on reproduction and immune function may have important demographic consequences on farmland bird populations. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25663614 [PubMed - as supplied by publisher]

13. Int J Biometeorol. 2015 Feb 7. [Epub ahead of print]

Empirical evidence of cold stress induced cell mediated and humoral immune response in common myna (Sturnus tristis).

Sandhu MA1, Zaib A, Anjum MS, Qayyum M.
Author information:
Department of Biomedical Sciences, Faculty of Veterinary and Animal Sciences, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan,


Common myna (Sturnus tristis) is a bird indigenous to the Indian subcontinent that has invaded many parts of the world. At the onset of our investigation, we hypothesized that the immunological profile of myna makes it resistant to harsh/new environmental conditions. In order to test this hypothesis, a number of 40 mynas were caught and divided into two groups, i.e., 7 and 25 °C for 14 days. To determine the effect of cold stress, cell mediated and humoral immune responses were assessed. The macrophage engulfment percentage was significantly (P < 0.05) higher at 25 °C rather than 7 °C either co-incubated with opsonized or unopsonized sheep red blood cells (SRBC). Macrophage engulfment/cell and nitric oxide production behaved in a similar manner. However, splenic cells plaque formation, heterophil to lymphocyte (H/L) ratio, and serum IgM or IgG production remained non-significant. There was a significant increase of IgG antibody production after a second immunization by SRBC. To the best of our knowledge, these findings have never been reported in the progression of this bird's invasion in frosty areas of the world. The results revealed a strengthened humoral immune response of myna and made this bird suitable for invasion in the areas of harsh conditions.
PMID: 25663442 [PubMed - as supplied by publisher]

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14. Trends Ecol Evol. 2015 Feb 3. pii: S0169-5347(15)00006-3. doi: 10.1016/j.tree.2015.01.004. [Epub ahead of print]

Autumn, the neglected season in climate change research.

Gallinat AS1, Primack RB2, Wagner DL3.
Author information:
Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA. Electronic address:
Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, U-43 Storrs, CT 06269, USA.


Autumn remains a relatively neglected season in climate change research in temperate and arctic ecosystems. This neglect occurs despite the importance of autumn events, including leaf senescence, fruit ripening, bird and insect migration, and induction of hibernation and diapause. Changes in autumn phenology alter the reproductive capacity of individuals, exacerbate invasions, allow pathogen amplification and higher disease-transmission rates, reshuffle natural enemy-prey dynamics, shift the ecological dynamics among interacting species, and affect the net productivity of ecosystems. We synthesize some of our existing understanding of autumn phenology and identify five areas ripe for future climate change research. We provide recommendations to address common pitfalls in autumnal research as well as to support the conservation and management of vulnerable ecosystems and taxa.
Copyright © 2015 Elsevier Ltd. All rights reserved.
PMID: 25662784 [PubMed - as supplied by publisher]

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15. Semin Cutan Med Surg. 2014 Sep;33(3):110-5.

Dermatoses associated with mites other than Sarcoptes.

Ken KM1, Shockman SC, Sirichotiratana M, Lent MP, Wilson ML.
Author information:
Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA.


Mites are arthropods of the subclass Acari (Acarina). Although Sarcoptes is the mite most commonly recognized as a cause of human skin disease in the United States, numerous other mite-associated dermatoses have been described, and merit familiarity on the part of physicians treating skin disease. This review discusses several non-scabies mites and their associated diseases, including Demodex, chiggers, Cheyletiella, bird mites, grain itch, oak leaf itch, grocer's itch, tropical rat mite, snake mite, and Psoroptes.
PMID: 25577848 [PubMed - indexed for MEDLINE]

16. Euro Surveill. 2014 Oct 23;19(42). pii: 20937.

Multiple human-to-human transmission from a severe case of psittacosis, Sweden, January-February 2013.

Wallensten A1, Fredlund H, Runehagen A.
Author information:
Public Health Agency of Sweden, Solna, Sweden.


Proven transmission of Chlamydia psittaci between humans has been described on only one occasion previously. We describe an outbreak which occurred in Sweden in early 2013, where the epidemiological and serological investigation suggests that one patient, severely ill with psittacosis after exposure to wild bird droppings, transmitted the disease to ten others: Two family members, one hospital roommate and seven hospital caregivers. Three cases also provided respiratory samples that could be analysed by PCR. All the obtained C. psittaci sequences were indistinguishable and clustered within genotype A. The finding has implications for the management of severely ill patients with atypical pneumonia, because these patients may be more contagious than was previously thought. In order to prevent nosocomial person-to-person transmission of C. psittaci, stricter hygiene measures may need to be applied.
Free Article
PMID: 25358043 [PubMed - indexed for MEDLINE]

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17. Sci Total Environ. 2015 Jan 1;502:60-9. doi: 10.1016/j.scitotenv.2014.09.006. Epub 2014 Sep 19.

Brominated flame retardant trends in aquatic birds from the Salish Sea region of the west coast of North America, including a mini-review of recent trends in marine and estuarine birds.

Miller A1, Elliott JE2, Elliott KH3, Guigueno MF3, Wilson LK4, Lee S5, Idrissi A6.
Author information:
Department of Applied Biology, University of British Columbia, 2357 Main Mall, Vancouver, BC, Canada.
Science and Technology, Environment Canada, Delta, BC V4K 3N2, Canada. Electronic address:
Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada.
Canadian Wildlife Service, Pacific Wildlife Research Centre, Environment Canada, Delta, BC V4K 3N2, Canada.
Science and Technology, Environment Canada, Delta, BC V4K 3N2, Canada.
Environment Canada, National Wildlife Research Centre, Ottawa, ON K1A 0H3, Canada.


Polybrominated diphenyl ethers (PBDEs) increased in many matrices during the 1990s and early 2000s. Since voluntary restrictions and regulations on PBDEs were implemented in North America circa early 2000s, decreases in PBDEs have occurred in many of these same matrices. To examine temporal trends in the North Pacific, we retrospectively analysed PBDEs and eight non-PBDE flame retardants (FR) in eggs of two aquatic bird species, great blue herons, Ardea herodias, and double-crested cormorants, Phalacrocorax auritus, collected along the British Columbia coast, Canada from 1979 to 2012. Increasing PBDE concentrations were observed in both species followed by significant decreases post-2000 for all dominant congeners and ΣPBDE. Non-PBDE FRs were generally undetected in cormorant eggs, or detected at very low levels in heron eggs, except for hexabromocyclododecane (HBCDD). HBCDD, currently unregulated in North America, was not detected in early sampling years; however low concentrations were observed in both species in recent sampling years (2003-2012). Dietary tracers (δ(13)C and δ(15)N) did not change significantly over time, indicating that temporal changes in PBDEs are likely caused by implemented regulations. A comparison with recently published temporal trends of ΣPBDE in marine birds from North America and Europe is given.
Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.
PMID: 25241209 [PubMed - indexed for MEDLINE]

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18. Philos Trans R Soc Lond B Biol Sci. 2014 Aug 5;369(1648). pii: 20130349. doi: 10.1098/rstb.2013.0349.

Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon.

Wessinger CA1, Hileman LC1, Rausher MD2.
Author information:
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
Department of Biology, Duke University, Durham, NC 27708, USA


Distinct floral pollination syndromes have emerged multiple times during the diversification of flowering plants. For example, in western North America, a hummingbird pollination syndrome has evolved more than 100 times, generally from within insect-pollinated lineages. The hummingbird syndrome is characterized by a suite of floral traits that attracts and facilitates pollen movement by hummingbirds, while at the same time discourages bee visitation. These floral traits generally include large nectar volume, red flower colour, elongated and narrow corolla tubes and reproductive organs that are exerted from the corolla. A handful of studies have examined the genetic architecture of hummingbird pollination syndrome evolution. These studies find that mutations of relatively large effect often explain increased nectar volume and transition to red flower colour. In addition, they suggest that adaptive suites of floral traits may often exhibit a high degree of genetic linkage, which could facilitate their fixation during pollination syndrome evolution. Here, we explore these emerging generalities by investigating the genetic basis of floral pollination syndrome divergence between two related Penstemon species with different pollination syndromes--bee-pollinated P. neomexicanus and closely related hummingbird-pollinated P. barbatus. In an F2 mapping population derived from a cross between these two species, we characterized the effect size of genetic loci underlying floral trait divergence associated with the transition to bird pollination, as well as correlation structure of floral trait variation. We find the effect sizes of quantitative trait loci for adaptive floral traits are in line with patterns observed in previous studies, and find strong evidence that suites of floral traits are genetically linked. This linkage may be due to genetic proximity or pleiotropic effects of single causative loci. Interestingly, our data suggest that the evolution of floral traits critical for hummingbird pollination was not constrained by negative pleiotropy at loci that show co-localization for multiple traits.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.
PMCID: PMC4071523 [Available on 2015-08-05]
PMID: 24958923 [PubMed - indexed for MEDLINE]

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19. J Environ Radioact. 2014 Sep;135:108-12. doi: 10.1016/j.jenvrad.2014.04.008. Epub 2014 May 7.

(210)Polonium and (210)lead content of marine birds from Southeastern Brazil.

Godoy JM1, Siciliano S2, de Carvalho ZL3, Tavares DC4, de Moura JF2, Godoy ML3.
Author information:
Instituto de Radioproteção e Dosimetria (IRD), Caixa Postal 37750, Barra da Tijuca, 22642-970 Rio de Janeiro, Brazil; Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marquês de São Vicente 225, 22453-900 Rio de Janeiro, Brazil. Electronic address:
Escola Nacional de Saúde Pública, FIOCRUZ, Dept° de Endemias, Grupo de Estudos de Mamíferos Marinhos da Região dos Lagos (GEMM-Lagos), Rua Leopoldo Bulhões, 1480-6° andar, Manguinhos, Rio de Janeiro, RJ 21410-210, Brazil.
Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marquês de São Vicente 225, 22453-900 Rio de Janeiro, Brazil.
Universidade Estadual do Norte Fluminense-UENF, CBB, Laboratório de Ciências Ambientais, Campos dos Goytacazes, RJ 28013-602, Brazil.


In this study, we report the (210)Po and (210)Pb concentrations of bone, muscle and liver samples that were obtained from twelve different marine bird species stranded on beaches in the central-north region of Rio de Janeiro State. Both radionuclides were highly concentrated in the liver samples; however, the lowest mean (210)Po/(210)Pb activity ratio (1.3) was observed in bones compared with liver and muscle (16.8 and 13.8, respectively). Among the species that were studied, Fregata magnificens, with a diet based exclusively on fish, had the lowest (210)Pb and (210)Po concentrations and the lowest (210)Po/(210)Pb activity ratio. The (210)Po concentrations in Puffinus spp. liver samples followed a log-normal distribution, with a geometric mean of 300 Bq kg(-1)wet weight. Only two references pertaining to (210)Po in marine birds were found in a Web of Science search of the literature, and each study reported a different concentration value. The values determined in this experiment are consistent with those in one of the previous studies, which also included one of the species studied in this work. No values for (210)Pb in marine birds have been published previously.
Copyright © 2014 Elsevier Ltd. All rights reserved.
PMID: 24814720 [PubMed - indexed for MEDLINE]

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