Stable multi-level social structure is maintained by habitat geometry in a wild bird population

ABSTRACTSocial structure can have profound evolutionary and ecological implications for animal populations. Structure can arise and be maintained via social preferences or be indirectly shaped by habitat structure. Understanding how social structure emerges is important for understanding the potential links between social structure and evolutionary and ecological processes. Here, we study a large community of wild birds fitted with uniquely-coded passive integrated transponder (PIT) tags and recorded on a grid of automated feeders fitted with radio frequency identification (RFID) antennae. We show that both large-scale and fine-scale network communities are consistent across years in this population, despite high generational turn-over. Studying the process that generates community structure, here the movement of individual birds across the woodland, suggests an important role of habitat geometry in shaping population-level social community structure. Our study highlights how relatively simple factors can produce apparent emergent social structure at the population scale, which has widespread implications for understanding eco-evolutionary dynamics.

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Distinguishing within from between individual effects: How to use the within-individual centering method for quadratic pattern

10.1101/2020.05.25.114421 ◽

2020 ◽

Author(s):

Rémi Fay ◽

Julien Martin ◽

Floriane Plard

Keyword(s):

Linear Relationship ◽

General Equation ◽

Evolutionary Dynamics ◽

Population Level ◽

List Type ◽

Ecological Processes ◽

Individual Pattern ◽

Individual Effects ◽

Non Linear ◽

The Individual

AbstractAny average pattern observed at the population level may confound two different processes: the within-individual process and the between-individual process. Separating within- from between-individual patterns is critical for our understanding of ecological processes and evolutionary dynamics.The within-individual centering method allows distinguishing within from between individual effects and this method has been largely used in ecology to investigate both linear and quadratic patterns. Here we show that two alternative equations could be used for the investigation of quadratic relationships and explain in which circumstances they are valid.We show that these two alternative equations make different assumptions about the shape of the individual pattern. Reviewing the literature, we find that the inappropriate equation has likely been applied by most of the studies investigated quadratic patterns.To investigate properly quadratic patterns using the within individual centering method, it is critical that the pattern assumed by the equation used is consistent with the biological pattern investigated. We illustrate this statement with the example of age-specific trajectories because age corresponds to the most frequent individual-centered variable used for quadratic pattern. Finally, we give the general equation of the within-individual centering method for any non-linear relationship.

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The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions

10.1101/2020.07.30.228205 ◽

2020 ◽

Author(s):

Peng He ◽

Pierre-Olivier Montiglio ◽

Marius Somveille ◽

Mauricio Cantor ◽

Damien R. Farine

Keyword(s):

Social Structure ◽

Structural Connectivity ◽

Population Level ◽

R Package ◽

Habitat Configuration ◽

Alternative Habitat ◽

Animal Populations ◽

Habitat Networks ◽

Animal Habitat

AbstractBy shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. For example, it is well known that the social structure of animal populations can shape spreading dynamics, but it remains underexplored to what extent such dynamics are determined by the underlying habitat configuration. To address this gap, we propose a framework and model inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animals’ habitats, and highlight the need for a bottom-up generative model that can depict realistic variations in habitat structural connectivity. Second, we describe a model for simulating animal habitat networks (available in the R package AnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we use our framework to demonstrate how transmission properties, such as the spread of a pathogen, can be impacted by both local connectivity and landscape-level characteristics of the habitat. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.

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Structural variation during dog domestication: insights from gray wolf and dhole genomes

National Science Review ◽

10.1093/nsr/nwy076 ◽

2018 ◽

Vol 6 (1) ◽

pp. 110-122 ◽

Cited By ~ 8

Author(s):

Guo-Dong Wang ◽

Xiu-Juan Shao ◽

Bing Bai ◽

Junlong Wang ◽

Xiaobo Wang ◽

...

Keyword(s):

Large Scale ◽

Evolutionary Dynamics ◽

De Novo ◽

Population Level ◽

Acid Synthesis ◽

Gray Wolf ◽

Structural Variations ◽

Cuon Alpinus ◽

New Genes ◽

Agricultural Revolution

Abstract Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.

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The labour that dare not speak its name

10.1093/oso/9780199355914.003.0003 ◽

2017 ◽

Author(s):

Jason Toynbee

Keyword(s):

Social Structure ◽

Large Scale ◽

Division Of Labour ◽

Concrete Material ◽

Material World ◽

Music Making ◽

Causal Impact ◽

Musical Creativity ◽

Material Conditions

The is chapter argues that to understand the distributed nature of musical creativity we need to examine its connection to large-scale social structure and to capitalist relations of labour. These relations have a ‘downward’ causal impact on creative acts. Firstly, this is through the division of labour, which plays out in different ways across genres from classical to pop. Secondly, creative musical labour involves engagement with the concrete, material world. The distributed nature of creativity is determined not only by the drive to divide or consolidate music-making tasks but also depends on the nature of the musical materials to hand, and methods of dealing with them. Two methods are described in this chapter: translation and intensification. Each (sometimes they are combined) entails the making of relatively autonomous creative choices which are emergent from the structural and material conditions of musical labour.

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The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions

Oecologia ◽

10.1007/s00442-021-04967-y ◽

2021 ◽

Author(s):

Peng He ◽

Pierre-Olivier Montiglio ◽

Marius Somveille ◽

Mauricio Cantor ◽

Damien R. Farine

Keyword(s):

Population Level ◽

R Package ◽

Habitat Configuration ◽

Modelling Framework ◽

Alternative Habitat ◽

Animal Populations ◽

Research Questions ◽

Habitat Networks ◽

Animal Habitat

AbstractBy shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. To address this gap, we propose a modelling framework inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animal habitats, and highlight the need for a bottom–up generative model that can depict realistic variations in habitat potential connectivity. Second, we describe a model for simulating animal habitat networks (available in the R package AnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we lay out three key research questions and demonstrate how our framework can address them. By simulating the spread of a pathogen within a population, we show how transmission properties can be impacted by both local potential connectivity and landscape-level characteristics of habitats. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.

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Mixture models as a method for comparative sociality: social networks and demographic change in resident killer whales

Behavioral Ecology and Sociobiology ◽

10.1007/s00265-021-03006-3 ◽

2021 ◽

Vol 75 (4) ◽

Author(s):

Samuel Ellis ◽

Daniel W. Franks ◽

Michael N. Weiss ◽

Michael A. Cant ◽

Paolo Domenici ◽

...

Keyword(s):

Mixture Models ◽

Demographic Change ◽

Social Preferences ◽

Social Bonds ◽

Killer Whales ◽

Animal Populations ◽

Binomial Mixture ◽

Opposite Sex ◽

Social Associations ◽

Social Association

Abstract In studies of social behaviour, social bonds are usually inferred from rates of interaction or association. This approach has revealed many important insights into the proximate formation and ultimate function of animal social structures. However, it remains challenging to compare social structure between systems or time-points because extrinsic factors, such as sampling methodology, can also influence the observed rate of association. As a consequence of these methodological challenges, it is difficult to analyse how patterns of social association change with demographic processes, such as the death of key social partners. Here we develop and illustrate the use of binomial mixture models to quantitatively compare patterns of social association between networks. We then use this method to investigate how patterns of social preferences in killer whales respond to demographic change. Resident killer whales are bisexually philopatric, and both sexes stay in close association with their mother in adulthood. We show that mothers and daughters show reduced social association after the birth of the daughter’s first offspring, but not after the birth of an offspring to the mother. We also show that whales whose mother is dead associate more with their opposite sex siblings and with their grandmother than whales whose mother is alive. Our work demonstrates the utility of using mixture models to compare social preferences between networks and between species. We also highlight other potential uses of this method such as to identify strong social bonds in animal populations. Significance statement Comparing patters of social associations between systems, or between the same systems at different times, is challenging due to the confounding effects of sampling and methodological differences. Here we present a method to allow social associations to be robustly classified and then compared between networks using binomial mixture models. We illustrate this method by showing how killer whales change their patterns of social association in response to the birth of calves and the death of their mother. We show that after the birth of her calf, females associate less with their mother. We also show that whales’ whose mother is dead associate more with their opposite sex siblings and grandmothers than whales’ whose mother is alive. This clearly demonstrates how this method can be used to examine fine scale temporal processes in animal social systems.

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Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Nature Communications ◽

10.1038/s41467-021-20958-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

H. De Kort ◽

J. G. Prunier ◽

S. Ducatez ◽

O. Honnay ◽

M. Baguette ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Evolutionary Dynamics ◽

Environmental Changes ◽

Peripheral Populations ◽

Plant Dispersal ◽

Weak Support ◽

Animal Populations ◽

Plant Groups ◽

Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

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214 Longitudinal Changes in Sleep Duration, Timing, Variability, and Stages during the COVID-19 Pandemic: Large-Scale Fitbit Data

SLEEP ◽

10.1093/sleep/zsab072.213 ◽

2021 ◽

Vol 44 (Supplement_2) ◽

pp. A86-A86

Author(s):

Michael Grandner ◽

Naghmeh Rezaei

Keyword(s):

New York ◽

Los Angeles ◽

San Francisco ◽

Sleep Duration ◽

Large Scale ◽

Age Groups ◽

Population Level ◽

Sleep Stages ◽

Longitudinal Changes ◽

Timing Variability

Abstract Introduction The COVID-19 pandemic has resulted in societal-level changes to sleep and other behavioral patterns. Objective, longitudinal data would allow for a greater understanding of sleep-related changes at the population level. Methods N= 163,524 deidentified active Fitbit users from 6 major US cities contributed data, representing areas particularly hard-hit by the pandemic (Chicago, Houston, Los Angeles, New York, San Francisco, and Miami). Sleep variables extracted include nightly and weekly mean sleep duration and bedtime, variability (standard deviation) of sleep duration and bedtime, and estimated arousals and sleep stages. Deviation from similar timeframes in 2019 were examined. All analyses were performed in Python. Results These data detail how sleep duration and timing changed longitudinally, stratified by age group and gender, relative to previous years’ data. Overall, 2020 represented a significant departure for all age groups and both men and women (P<0.00001). Mean sleep duration increased in nearly all groups (P<0.00001) by 5-11 minutes, compared to a mean decrease of 5-8 minutes seen over the same period in 2019. Categorically, sleep duration increased for some and decreased for others, but more extended than restricted. Sleep phase shifted later for nearly all groups (p<0.00001). Categorically, bedtime was delayed for some and advanced for others, though more delayed than advanced. Duration and bedtime variability decreased, owing largely to decreased weekday-weekend differences. WASO increased, REM% increased, and Deep% decreased. Additional analyses show stratified, longitudinal changes to sleep duration and timing mean and variability distributions by month, as well as effect sizes and correlations to other outcomes. Conclusion The pandemic was associated with increased sleep duration on average, in contrast to 2019 when sleep decreased. The increase was most profound among younger adults, especially women. The youngest adults also experienced the greatest bedtime delay, in line with extensive school-start-times and chronotype data. When given the opportunity, the difference between weekdays and weekends became smaller, with occupational implications. Sleep staging data showed that slightly extending sleep minimally impacted deep sleep but resulted in a proportional increase in REM. Wakefulness during the night also increased, suggesting increased arousal despite greater sleep duration. Support (if any) This research was supported by Fitbit, Inc.

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A review of passive self-sensing tag

Sensor Review ◽

10.1108/sr-01-2017-0001 ◽

2017 ◽

Vol 37 (3) ◽

pp. 338-345 ◽

Cited By ~ 4

Author(s):

Yawei Xu ◽

Lihong Dong ◽

Haidou Wang ◽

Jiannong Jing ◽

Yongxiang Lu

Keyword(s):

Radio Frequency Identification ◽

Large Scale ◽

Low Cost ◽

Integrated Sensor ◽

Content Type ◽

Passive Sensing ◽

Static Information ◽

Potential Applications ◽

Frequency Identification ◽

Identification Tags

Purpose Radio frequency identification tags for passive sensing have attracted wide attention in the area of Internet of Things (IoT). Among them, some tags can sense the property change of objects without an integrated sensor, which is a new trend of passive sensing based on tag. The purpose of this paper is to review recent research on passive self-sensing tags (PSSTs). Design/methodology/approach The PSSTs reported in the past decade are classified in terms of sensing mode, composition and the ways of power supply. This paper presents operation principles of PSSTs and analyzes the characteristics of them. Moreover, the paper focuses on summarizing the latest sensing parameters of PSSTs and their matching equipment. Finally, some potential applications and challenges faced by this emerging technique are discussed. Findings PSST is suitable for long-term and large-scale monitoring compared to conventional sensors because it gets rid of the limitation of battery and has relatively low cost. Also, the static information of objects stored in different PSSTs can be identified by a single reader without touch. Originality/value This paper provides a detailed and timely review of the rapidly growing research in PSST.

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Survey on Prominent RFID Authentication Protocols for Passive Tags

Sensors ◽

10.3390/s18103584 ◽

2018 ◽

Vol 18 (10) ◽

pp. 3584 ◽

Cited By ~ 10

Author(s):

Rania Baashirah ◽

Abdelshakour Abuzneid

Keyword(s):

Radio Frequency Identification ◽

Large Scale ◽

Security Requirements ◽

The Internet ◽

Authentication Protocols ◽

Reliable System ◽

Passive Tags ◽

Frequency Identification ◽

Rfid Authentication Protocols ◽

The Internet Of Things

Radio Frequency Identification (RFID) is one of the leading technologies in the Internet of Things (IoT) to create an efficient and reliable system to securely identify objects in many environments such as business, health, and manufacturing areas. Recent RFID authentication protocols have been proposed to satisfy the security features of RFID communication. In this article, we identify and review some of the most recent and enhanced authentication protocols that mainly focus on the authentication between a reader and a tag. However, the scope of this survey includes only passive tags protocols, due to the large scale of the RFID framework. We examined some of the recent RFID protocols in term of security requirements, computation, and attack resistance. We conclude that only five protocols resist all of the major attacks, while only one protocol satisfies all of the security requirements of the RFID system.

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