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Coste CFD, Bienvenu F, Ronget V, Ramirez-Loza JP, Cubaynes S, Pavard S. The kinship matrix: inferring the kinship structure of a population from its demography. Ecol Lett 2021; 24:2750-2762. [PMID: 34609786 DOI: 10.1111/ele.13854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022]
Abstract
The familial structure of a population and the relatedness of its individuals are determined by its demography. There is, however, no general method to infer kinship directly from the life cycle of a structured population. Yet, this question is central to fields such as ecology, evolution and conservation, especially in contexts where there is a strong interdependence between familial structure and population dynamics. Here, we give a general formula to compute, from any matrix population model, the expected number of arbitrary kin (sisters, nieces, cousins, etc) of a focal individual ego, structured by the class of ego and of its kin. Central to our approach are classic but little-used tools known as genealogical matrices. Our method can be used to obtain both individual-based and population-wide metrics of kinship, as we illustrate. It also makes it possible to analyse the sensitivity of the kinship structure to the traits implemented in the model.
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Affiliation(s)
- Christophe F D Coste
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - François Bienvenu
- Department of Mathematics and Computer Science, Transilvania University of Braşov, Braşov, Romania.,Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,UMR AGAP, Université de Montpellier, CIRAD, INRAE, L'institut Agro, Montpellier, France.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Victor Ronget
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| | - Juan-Pablo Ramirez-Loza
- CEFE, CNRS, Univ. Montpellier, Univ. Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sarah Cubaynes
- CEFE, CNRS, Univ. Montpellier, Univ. Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Samuel Pavard
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
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Layton-Matthews K, Griesser M, Coste CFD, Ozgul A. Forest management affects seasonal source-sink dynamics in a territorial, group-living bird. Oecologia 2021; 196:399-412. [PMID: 34061249 PMCID: PMC8241677 DOI: 10.1007/s00442-021-04935-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/03/2021] [Indexed: 12/03/2022]
Abstract
The persistence of wildlife populations is under threat as a consequence of human activities, which are degrading natural ecosystems. Commercial forestry is the greatest threat to biodiversity in boreal forests. Forestry practices have degraded most available habitat, threatening the persistence of natural populations. Understanding population responses is, therefore, critical for their conservation. Population viability analyses are effective tools to predict population persistence under forestry management. However, quantifying the mechanisms driving population responses is complex as population dynamics vary temporally and spatially. Metapopulation dynamics are governed by local dynamics and spatial factors, potentially mediating the impacts of forestry e.g., through dispersal. Here, we performed a seasonal, spatially explicit population viability analysis, using long-term data from a group-living territorial bird (Siberian jay, Perisoreus infaustus). We quantified the effects of forest management on metapopulation dynamics, via forest type-specific demography and spatially explicit dispersal, and how forestry impacted the stability of metapopulation dynamics. Forestry reduced metapopulation growth and stability, through negative effects on reproduction and survival. Territories in higher quality natural forest contributed more to metapopulation dynamics than managed forests, largely through demographic processes rather than dispersal. Metapopulation dynamics in managed forest were also less resilient to disturbances and consequently, may be more vulnerable to environmental change. Seasonal differences in source-sink dynamics observed in managed forest, but not natural forests, were caused by associated seasonal differences in dispersal. As shown here, capturing seasonal source-sink dynamics allows us to predict population persistence under human disturbance and to provide targeted conservation recommendations.
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Affiliation(s)
- Kate Layton-Matthews
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
- Norwegian Institute for Nature Research, Tromsø, Norway.
| | - Michael Griesser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christophe F D Coste
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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3
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Pavard S, Coste CFD. Evolutionary demographic models reveal the strength of purifying selection on susceptibility alleles to late-onset diseases. Nat Ecol Evol 2021; 5:392-400. [PMID: 33398109 DOI: 10.1038/s41559-020-01355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023]
Abstract
Assessing the role played by purifying selection on a susceptibility allele to late-onset disease (SALOD) is crucial to understanding the puzzling allelic spectrum of a disease, because most alleles are recent and rare. This fact is surprising because it suggests that alleles are under purifying selection while those that are involved in post-menopause mortality are often considered neutral in the genetic literature. The aim of this article is to use an evolutionary demography model to assess the magnitude of selection on SALODs while accounting for epidemiological and sociocultural factors. We develop an age-structured population model allowing for the calculation of SALOD selection coefficients (1) for a large and realistic parameter space for disease onset, (2) in a two-sex model in which men can reproduce in old age and (3) for situations in which child survival depends on maternal, paternal and grandmaternal care. The results show that SALODs are under purifying selection for most known age-at-onset distributions of late-onset genetic diseases. Estimates regarding various genes involved in susceptibility to cancer or Huntington's disease demonstrate that negative selection largely overcomes the effects of drift in most human populations. This is also probably true for neurodegenerative or polycystic kidney diseases, although sociocultural factors modulate the effect of selection in these cases. We conclude that neutrality is probably the exception among alleles that have a deleterious effect in old age and that accounting for sociocultural factors is required to understand the full extent of the force of selection shaping senescence in humans.
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Affiliation(s)
- Samuel Pavard
- Unité 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Paris, France.
| | - Christophe F D Coste
- Unité 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Paris, France.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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5
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Spagopoulou F, Teplitsky C, Lind MI, Chantepie S, Gustafsson L, Maklakov AA. Silver-spoon upbringing improves early-life fitness but promotes reproductive ageing in a wild bird. Ecol Lett 2020; 23:994-1002. [PMID: 32239642 DOI: 10.1111/ele.13501] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 01/07/2023]
Abstract
Early-life conditions can have long-lasting effects and organisms that experience a poor start in life are often expected to age at a faster rate. Alternatively, individuals raised in high-quality environments can overinvest in early-reproduction resulting in rapid ageing. Here we use a long-term experimental manipulation of early-life conditions in a natural population of collared flycatchers (Ficedula albicollis), to show that females raised in a low-competition environment (artificially reduced broods) have higher early-life reproduction but lower late-life reproduction than females raised in high-competition environment (artificially increased broods). Reproductive success of high-competition females peaked in late-life, when low-competition females were already in steep reproductive decline and suffered from a higher mortality rate. Our results demonstrate that 'silver-spoon' natal conditions increase female early-life performance at the cost of faster reproductive ageing and increased late-life mortality. These findings demonstrate experimentally that natal environment shapes individual variation in reproductive and actuarial ageing in nature.
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Affiliation(s)
- Foteini Spagopoulou
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvagen 18D, 75236, Uppsala, Sweden
| | - Céline Teplitsky
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Martin I Lind
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvagen 18D, 75236, Uppsala, Sweden
| | - Stéphane Chantepie
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Lars Gustafsson
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvagen 18D, 75236, Uppsala, Sweden
| | - Alexei A Maklakov
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvagen 18D, 75236, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Coste CF, Pavard S. Analysis of a multitrait population projection matrix reveals the evolutionary and demographic effects of a life history trade-off. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2019.108915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cohen AA, Coste CFD, Li X, Bourg S, Pavard S. Are trade‐offs really the key drivers of ageing and life span? Funct Ecol 2019. [DOI: 10.1111/1365-2435.13444] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan A. Cohen
- Groupe de recherche PRIMUS Department of Family Medicine University of Sherbrooke Sherbrooke QC Canada
| | - Christophe F. D. Coste
- Center for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Unité Eco‐anthropologie (EA) Muséum National d'Histoire Naturelle CNRS 7206 Université Paris Diderot Paris France
| | - Xiang‐Yi Li
- Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Salomé Bourg
- CNRS Laboratoire de Biométrie et Biologie Évolutive UMR5558 Université Lyon 1 Villeurbanne France
| | - Samuel Pavard
- Unité Eco‐anthropologie (EA) Muséum National d'Histoire Naturelle CNRS 7206 Université Paris Diderot Paris France
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