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Article ; Online: Characterization of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (

François, Sarah / Hill, Sarah C / Perrins, Christopher M / Pybus, Oliver G

Microbiology resource announcements

2024 Volume 13, Issue 3, Page(s) e0118623

Abstract: We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic ... ...

Abstract	We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic surveillance of mute swan (
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.01186-23
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Article ; Online: Disentangling the causes of age‐assortative mating in bird populations with contrasting life‐history strategies

Woodman, Joe P. / Cole, Ella F. / Firth, Josh A. / Perrins, Christopher M. / Sheldon, Ben C.

Journal of Animal Ecology. 2023 May, v. 92, no. 5 p.979-990

2023

Abstract: Age shapes fundamental processes related to behaviour, survival and reproduction, where age influences reproductive success, non‐random mating with respect to age can magnify or mitigate such effects. Consequently, the correlation in partners' age across ...

Abstract	Age shapes fundamental processes related to behaviour, survival and reproduction, where age influences reproductive success, non‐random mating with respect to age can magnify or mitigate such effects. Consequently, the correlation in partners' age across a population may influence its productivity. Despite widespread evidence for age‐assortative mating, little is known about what drives this assortment and its variation. Specifically, the relative importance of active (same‐age mate preference) and passive processes (assortment as a consequence of other spatial or temporal effects) in driving age assortment is not well understood. In this paper, we compare breeding data from a great tit and mute swan population (51‐ and 31‐year datasets, respectively) to tease apart the contributions of pair retention, cohort age structure and active age‐related mate selection to age assortment in species with contrasting life histories. Both species show age‐assortative mating and variable assortment between years. However, we demonstrate that the drivers of age assortment differ between the species, as expected from their life histories and resultant demographic differences. In great tits, pair fidelity has a weak effect on age‐assortative mating through pair retention; variation in age assortment is primarily driven by fluctuations in age structure from variable juvenile recruitment. Age‐assortative mating is, therefore, largely passive, with no evidence consistent with active age‐related mate selection. In mute swans, age assortment is partly explained by pair retention, but not population age structure, and evidence exists for active age‐assortative pairing. This difference is likely to result from shorter life‐spans in great tits compared with mute swans, leading to fundamental differences in their population age structure, whereby a larger proportion of great tit populations consist of a single age cohort. In mute swans, age‐assortative pairing through mate selection may also be driven by greater age‐dependent variation in fitness. The study highlights the importance of considering how different life histories and demographic differences arising from these affect population processes that appear congruent across species. We suggest that future research should focus on uncovering the proximate mechanisms that lead to variation in active age‐assortative mate selection (as seen in mute swans); and the consequences of variation in age structure on the ecological and social functioning of wild populations.
Keywords	Cygnus olor ; Parus major ; age structure ; animal ecology ; birds ; data collection ; juveniles ; life history ; mating behavior ; reproductive success
Language	English
Dates of publication	2023-05
Size	p. 979-990.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13851
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Article ; Online: Disentangling the causes of age-assortative mating in bird populations with contrasting life-history strategies.

Woodman, Joe P / Cole, Ella F / Firth, Josh A / Perrins, Christopher M / Sheldon, Ben C

The Journal of animal ecology

2022 Volume 92, Issue 5, Page(s) 979–990

Abstract: Age shapes fundamental processes related to behaviour, survival and reproduction, where age influences reproductive success, non-random mating with respect to age can magnify or mitigate such effects. Consequently, the correlation in partners' age across ...

Abstract	Age shapes fundamental processes related to behaviour, survival and reproduction, where age influences reproductive success, non-random mating with respect to age can magnify or mitigate such effects. Consequently, the correlation in partners' age across a population may influence its productivity. Despite widespread evidence for age-assortative mating, little is known about what drives this assortment and its variation. Specifically, the relative importance of active (same-age mate preference) and passive processes (assortment as a consequence of other spatial or temporal effects) in driving age assortment is not well understood. In this paper, we compare breeding data from a great tit and mute swan population (51- and 31-year datasets, respectively) to tease apart the contributions of pair retention, cohort age structure and active age-related mate selection to age assortment in species with contrasting life histories. Both species show age-assortative mating and variable assortment between years. However, we demonstrate that the drivers of age assortment differ between the species, as expected from their life histories and resultant demographic differences. In great tits, pair fidelity has a weak effect on age-assortative mating through pair retention; variation in age assortment is primarily driven by fluctuations in age structure from variable juvenile recruitment. Age-assortative mating is, therefore, largely passive, with no evidence consistent with active age-related mate selection. In mute swans, age assortment is partly explained by pair retention, but not population age structure, and evidence exists for active age-assortative pairing. This difference is likely to result from shorter life-spans in great tits compared with mute swans, leading to fundamental differences in their population age structure, whereby a larger proportion of great tit populations consist of a single age cohort. In mute swans, age-assortative pairing through mate selection may also be driven by greater age-dependent variation in fitness. The study highlights the importance of considering how different life histories and demographic differences arising from these affect population processes that appear congruent across species. We suggest that future research should focus on uncovering the proximate mechanisms that lead to variation in active age-assortative mate selection (as seen in mute swans); and the consequences of variation in age structure on the ecological and social functioning of wild populations.
MeSH term(s)	Animals ; Mating Preference, Animal ; Reproduction ; Life History Traits ; Passeriformes
Language	English
Publishing date	2022-12-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13851
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Article ; Online: Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild.

François, Sarah / Nazki, Salik / Vickers, Stephen H / Fournié, Guillaume / Perrins, Christopher M / Broadbent, Andrew J / Pybus, Oliver G / Hill, Sarah C

The Journal of general virology

2023 Volume 104, Issue 8

Abstract: Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. ...

Abstract	Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (
MeSH term(s)	Humans ; Animals ; Gammacoronavirus/genetics ; Coronavirus/genetics ; Disease Outbreaks ; Anseriformes ; Coronavirus Infections/epidemiology ; Coronavirus Infections/veterinary ; Animals, Wild ; Genetic Variation ; Recombination, Genetic
Language	English
Publishing date	2023-07-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.001883
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Article ; Online: Impact of host age on viral and bacterial communities in a waterbird population.

Hill, Sarah C / François, Sarah / Thézé, Julien / Smith, Adrian L / Simmonds, Peter / Perrins, Christopher M / van der Hoek, Lia / Pybus, Oliver G

The ISME journal

2022 Volume 17, Issue 2, Page(s) 215–226

Abstract: Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level ... ...

Abstract	Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.
MeSH term(s)	Humans ; Animals ; Animals, Wild ; Birds ; Anseriformes ; Metagenome
Language	English
Publishing date	2022-11-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-022-01334-4
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Book: The Princeton encyclopedia of birds

Perrins, Christopher M

2009

Author's details	edited by Christopher Perrins
Keywords	Birds
Language	English
Dates of publication	2009-2003
Size	656 p. :, ill. (chiefly col.), col. maps ;, 27 cm.
Publisher	Princeton University Press
Publishing place	Princeton, N.J
Document type	Book
Note	Originally published as: The new encyclopedia of birds. 2003, c2004.
ISBN	9780691140704 ; 0691140707
Database	NAL-Catalogue (AGRICOLA)

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Book: The encyclopedia of birds

Perrins, Christopher M

2009

Author's details	edited by Christopher Perrins
Keywords	Birds
Language	English
Size	656 p. :, ill. (some col.), col. maps ;, 27 cm.
Publisher	Oxford University Press
Publishing place	Oxford ; New York
Document type	Book
ISBN	9780199568000 ; 0199568006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Sampling strategies for species with high breeding-site fidelity: A case study in burrow-nesting seabirds.

Arneill, Gavin E / Perrins, Christopher M / Wood, Matt J / Murphy, David / Pisani, Luca / Jessopp, Mark J / Quinn, John L

PloS one

2019 Volume 14, Issue 8, Page(s) e0221625

Abstract: Sampling approaches used to census and monitor populations of flora and fauna are diverse, ranging from simple random sampling to complex hierarchal stratified designs. Usually the approach taken is determined by the spatial and temporal distribution of ... ...

Abstract	Sampling approaches used to census and monitor populations of flora and fauna are diverse, ranging from simple random sampling to complex hierarchal stratified designs. Usually the approach taken is determined by the spatial and temporal distribution of the study population, along with other characteristics of the focal species. Long-term monitoring programs used to assess seabird population trends are facilitated by their high site fidelity, but are often hampered by large and difficult to access colonies, with highly variable densities that require intensive survey. We aimed to determine the sampling effort required to (a) estimate population size with a high degree of confidence, and (b) detect different scenarios of population change in a regionally important species in the Atlantic, the Manx shearwater (Puffinus puffinus). Analyses were carried out using data collected from tape-playback surveys on four islands in the North Atlantic. To explore how sampling effort influenced confidence around abundance estimates, we used the heuristic approach of imagining the areas sampled represented the total population, and bootstrapped varying proportions of subsamples. This revealed that abundance estimates vary dramatically when less than half of all plots (n dependent on the size of the site) is randomly subsampled, leading to an unacceptable lack of confidence in population estimates. Confidence is substantially improved using a multi-stage stratified approach based on previous information on distribution in the colonies. In reality, this could lead to reducing the number of plots required by up to 80%. Furthermore, power analyses suggested that random selection of monitoring plots using a matched pairs approach generates little power to detect overall population changes of 10%, and density-dependent changes as large as 50%, because variation in density between plots is so high. Current monitoring programs have a high probability of failing to detect population-level changes due to inappropriate sampling efforts. Focusing sampling in areas of high density with low plot to plot variance dramatically increases the power to detect year to year population change, albeit at the risk of not detecting increases in low density areas, which may be an unavoidable strategy when resources are limited. We discuss how challenging populations with similar features to seabirds might be censused and monitored most effectively.
MeSH term(s)	Animals ; Birds/physiology ; Breeding ; Geography ; Ireland ; Nesting Behavior/physiology ; Population Dynamics ; Species Specificity ; Surveys and Questionnaires ; Wales
Language	English
Publishing date	2019-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0221625
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Article ; Online: Who wears the pants in a mute swan pair? Deciphering the effects of male and female age and identity on breeding success.

Auld, Josh R / Perrins, Christopher M / Charmantier, Anne

The Journal of animal ecology

2013 Volume 82, Issue 4, Page(s) 826–835

Abstract: Traditionally, many breeding traits (e.g. the timing and size of clutches) were considered to be female-only traits in that males played little-to-no role in their expression. Although the contribution of males to such breeding traits, as well as other ... ...

Abstract	Traditionally, many breeding traits (e.g. the timing and size of clutches) were considered to be female-only traits in that males played little-to-no role in their expression. Although the contribution of males to such breeding traits, as well as other aspects of reproduction, is increasingly recognized, few studies have demonstrated the effects of male age and life history on breeding traits and, importantly, whether these effects are underlined by additive-genetic variation. Here, we take advantage of a long-term data set on mute swans (Cygnus olor) to demonstrate that the ages of both the male and female parents play significant roles in the timing and size of clutches, although recruitment success did not show similar effects. Individual males varied significantly in their influence on the timing of egg laying. We decomposed this variation using an 'animal model'; competing models that were the source of this variation as additive-genetic or permanent-environmental variation was not statistically distinguishable. Our results add to the growing evidence that reproductive performance should be considered as a product of the identity and condition of both parents.
MeSH term(s)	Aging ; Animals ; Anseriformes/physiology ; Female ; Linear Models ; Male ; Models, Biological ; Sexual Behavior, Animal/physiology
Language	English
Publishing date	2013-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.12043
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Article ; Online: Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.

Hill, Sarah C / Hansen, Rowena / Watson, Samantha / Coward, Vivien / Russell, Christine / Cooper, Jayne / Essen, Steve / Everest, Holly / Parag, Kris V / Fiddaman, Steven / Reid, Scott / Lewis, Nicola / Brookes, Sharon M / Smith, Adrian L / Sheldon, Ben / Perrins, Christopher M / Brown, Ian H / Pybus, Oliver G

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2019 Volume 374, Issue 1775, Page(s) 20180259

Abstract: Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and ...

Abstract	Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and temporal scales. However, information about the detailed dynamics and demographics of individual outbreaks in wild birds is rare and important epidemiological parameters remain unknown. We present data from a wild population of long-lived birds (mute swans; Cygnus olor) that has experienced three outbreaks of related H5 HPAIVs in the past decade, specifically, H5N1 (2007), H5N8 (2016) and H5N6 (2017). Detailed demographic data were available and intense sampling was conducted before and after the outbreaks; hence the population is unusually suitable for exploring the natural epidemiology, evolution and ecology of HPAIV in wild birds. We show that key epidemiological features remain remarkably consistent across multiple outbreaks, including the timing of virus incursion and outbreak duration, and the presence of a strong age-structure in morbidity that likely arises from an equivalent age-structure in immunological responses. The predictability of these features across a series of outbreaks in a complex natural population is striking and contributes to our understanding of HPAIV in wild birds. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
MeSH term(s)	Animals ; Animals, Wild/virology ; Anseriformes/virology ; Disease Outbreaks ; Influenza A Virus, H5N1 Subtype/classification ; Influenza A Virus, H5N1 Subtype/genetics ; Influenza A Virus, H5N1 Subtype/isolation & purification ; Influenza A virus/classification ; Influenza A virus/isolation & purification ; Influenza in Birds/epidemiology ; Influenza in Birds/mortality ; Influenza in Birds/virology ; Phylogeny ; United Kingdom/epidemiology
Language	English
Publishing date	2019-05-06
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2018.0259
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