11,750 results on '"Evolutionary biology"'
Search Results
2. Studies from Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) Have Provided New Data on Molecular Biology (New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans)
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Transposons ,Biology ,Genomes ,Genomics ,DNA sequencing ,Anopheles ,Molecular biology ,Evolutionary biology ,Population biology ,Editors ,Computational biology ,Health - Abstract
2019 JUL 19 (NewsRx) -- By a News Reporter-Staff News Editor at Health & Medicine Week -- New research on Biology - Molecular Biology is the subject of a report. [...]
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- 2019
3. The phylogeography debate and the epistemology of model-based evolutionary biology.
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Arroyo-Santos, Alfonso, Olson, Mark, and Vergara-Silva, Francisco
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PHYLOGEOGRAPHY , *BIOLOGICAL evolution , *THEORY of knowledge , *POPULATION biology , *STATISTICS - Abstract
Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes from the primary biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out-as a preliminary step in preparation for upcoming, more detailed treatments-the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute. [ABSTRACT FROM AUTHOR]
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- 2014
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4. The Adaptive Landscape in Evolutionary Biology
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Erik I. Svensson and Ryan Calsbeek
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Part iii ,Evolutionary biology ,Fitness landscape ,Genetic algorithm ,Population biology ,Biology ,Macroevolution ,Sewall wright ,Shifting balance theory - Abstract
PART I: HISTORICAL BACKGROUND AND PHILOSOPHICAL PERSPECTIVES PART II: CONTROVERSIES: FISHER'S FUNDAMENTAL THEORY VERSUS SEWALL WRIGHT'S SHIFTING BALANCE THEORY PART III: APPLICATIONS: MICROEVOLUTIONARY DYNAMICS, QUANTITATIVE GENETICS, AND POPULATION BIOLOGY PART IV: SPECIATION AND MACROEVOLUTION PART V: DEVELOPMENT, FORM, AND FUNCTION PART VI: CONCLUDING REMARKS
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- 2013
5. Contributions of single-cell genomics to our understanding of planktonic marine archaea
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Santoro, AE, Kellom, M, and Laperriere, SM
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Life Below Water ,Archaea ,Genome ,Archaeal ,Genomics ,Plankton ,Single-Cell Analysis ,thaumarchaea ,MGI archaea ,MGII archaea ,population biology ,Medical and Health Sciences ,Evolutionary Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.
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- 2019
6. Evolutionary biology of cancer
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Crespi, Bernard and Summers, Kyle
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EVOLUTIONARY theories , *HUMAN ecology , *BIOLOGY , *POPULATION biology - Abstract
Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease. [Copyright &y& Elsevier]
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- 2005
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7. Animal Behavior, Population Biology and the Modern Synthesis (1955–1985)
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Grodwohl, Jean-Baptiste
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- 2019
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8. Stable Models and Causal Explanation in Evolutionary Biology.
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Glymour, Bruce
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BIOLOGICAL evolution , *POPULATION biology , *MARKOV processes , *STOCHASTIC processes , *PHILOSOPHY of science - Abstract
Models that fail to satisfy the Markov condition are unstable because changes in state variable values may cause changes in the values of background variables, and these changes in background lead to predictive error. Such error arises because non-Markovian models fail to track the causal relations generating the values of response variables. This has implications for discussions of the level of selection: under certain plausible conditoins most standard models of group selection will not satisfy the Markov condition when fit to data from real populations. These models neither correctly represent the causal structure generating nor correctly explain the phenomena of interest. [ABSTRACT FROM AUTHOR]
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- 2008
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9. Population biology and evolutionary ecology in France: current state and prospects. Plenary address given at the founding congress of the European Society for Evolutionary Biology, 26 August 1987, in Basel
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Robert Barbault
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Functional ecology ,Evolutionary physiology ,Evolutionary anthropology ,Evolutionary biology ,Ecology (disciplines) ,Evolutionary ecology ,Population biology ,Economic geography ,Biology ,Applications of evolution ,Ecology and Evolutionary Biology ,Ecology, Evolution, Behavior and Systematics - Published
- 1988
10. How to Study Adaptation (and Why To Do It That Way)
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Olson, Mark E. and Arroyo-Santos, Alfonso
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- 2015
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11. GENERAL CONCEPTS ON THE EVOLUTIONARY BIOLOGY OF PARASITES
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Peter W. Price
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0106 biological sciences ,0301 basic medicine ,Ecology ,Ecology (disciplines) ,Parasitism ,Zoology ,Population biology ,Biology ,010603 evolutionary biology ,01 natural sciences ,Predation ,03 medical and health sciences ,030104 developmental biology ,Parasitology ,Evolutionary biology ,Adaptive radiation ,Genetics ,Evolutionary ecology ,General Agricultural and Biological Sciences ,Entomophagous parasite ,Ecology, Evolution, Behavior and Systematics - Abstract
Parasitism is a very common way of life, and probably the prevalent means of obtaining food among organisms. Adaptive radiation among parasites has been extensive, and yet ecological and evolutionary concepts on parasitism are poorly developed. Although Elton (1927) devoted a chapter in his pioneering ecology book to parasitism his conclusion was that the resemblances between predators and parasites are more important than the differences. This attitude is now prevalent in ecology texts (e.g. Andrewartha and Birch, 1954; Odum, 1971; Krebs, 1972; Colinvaux, 1973), and although much attention is devoted to predation, parasitism is almost ignored. Therefore, by using the inductive process, this paper attempts a synthesis of ecology and parasitology, the need for which has been recognized by Kennedy (1975), and it explores the evolutionary implications of parasite ecology. This synthesis should contribute to an understanding of parasites in three ways. First, a reevaluation of the abundance of parasitic species is made. Arndt (1940) estimated that 25% of animals in Germany are parasitic on others. Rothschild and Clay (1952) stated that parasitic animals probably exceed nonparasitic species in number of species and individuals, but provided little numerical support. A careful quantitative evaluation by Askew (1971) provided an estimate that 15% of insects, and 10% of all animal species are parasitic insects. Calculations presented in this paper indicate that well over 50% of the species of organisms extant today are parasitic. Second, general concepts on the ecology and evolution of parasites are presented, being derived from a combination of population biology, evolutionary theory and parasite biology. Third, predictions derived from the general concepts act as a guide to critical characteristics of parasite biology which need to be examined and tested in natural populations.
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- 1976
12. Ecology of the gyrfalcon (Falco rusticolus) in central Scandinavia: diet and feeding behaviour in fluctuating ptarmigan abundances
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Østnes, Jan Eivind, Slettenhaar, Annabel, and Nilsen, Erlend B.
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Ornithology ,Population Biology ,Terrestrial and Aquatic Ecology ,Animal Sciences ,Ecology and Evolutionary Biology ,Life Sciences ,Climate change ,Food-web dynamics ,Behavior and Ethology ,Predator-prey interactions ,Biology - Abstract
Due to climate change global temperatures are rising, which is particularly pronounced at higher latitudes. Therefore, it is important to investigate the resilience of northern ecosystems to these environmental changes. Predator-prey interactions are at the foundation of food-web dynamics in an ecosystem, making them increasingly relevant to study in the context of climate change. A predator-prey couple reflecting the dynamics of the boreal ecosystem in central Scandinavia is the gyrfalcon (Falco rusticolus) and the willow ptarmigan (Lagopus lagopus). Both show circumpolar breeding distributions which largely overlap. In this study we will describe the diet and feeding behaviour of the gyrfalcon in central Norway during the nesting stage. Previous studies have shown that gyrfalcons specialise on ptarmigan as prey throughout the year, but occasionally switch to other prey species depending on the season and area. We will also investigate how spring and summer conditions affect gyrfalcon diet, feeding behaviour and reproductive success. Climate change may alter the availability of prey for the gyrfalcons, so to investigate the ability of the gyrfalcons to switch to other prey types, we will also quantify the numerical and functional response of gyrfalcons to fluctuating ptarmigan abundances.
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- 2023
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13. Supplement: Improved inferences about landscape connectivity from spatial capture-recapture by integration of a movement model
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Dupont, Gates, Linden, Daniel, and Sutherland, Chris
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Statistics and Probability ,Other Ecology and Evolutionary Biology ,Population Biology ,Statistical Models ,Applied Statistics ,Design of Experiments and Sample Surveys ,Natural Resources and Conservation ,Ecology and Evolutionary Biology ,Physical Sciences and Mathematics ,Life Sciences ,Environmental Sciences - Abstract
Supplemental code for Dupont et al. 2021 "Improved inferences about landscape connectivity from spatial capture-recapture by integration of a movement model" published in Ecology (DOI: xxxx))
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- 2022
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14. Socially Defined Subpopulations Reveal Demographic Variation in a Giraffe Metapopulation
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Bond, Monica L, König, Barbara, Ozgul, A, Farine, Damien R, Lee, Derek E, University of Zurich, and Bond, Monica L
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0106 biological sciences ,Metapopulation ,Population biology ,Biology ,010603 evolutionary biology ,01 natural sciences ,Population density ,2309 Nature and Landscape Conservation ,Predation ,10127 Institute of Evolutionary Biology and Environmental Studies ,03 medical and health sciences ,ddc:570 ,media_common.cataloged_instance ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,General Environmental Science ,media_common ,2. Zero hunger ,0303 health sciences ,Ideal free distribution ,Ecology ,Reproductive success ,15. Life on land ,1105 Ecology, Evolution, Behavior and Systematics ,Habitat ,570 Life sciences ,biology ,590 Animals (Zoology) ,General Earth and Planetary Sciences ,2303 Ecology ,Giraffa camelopardalis ,Demography - Abstract
Populations are typically defined as spatially contiguous sets of individuals, but large populations of social species can be composed of discrete social communities that often overlap in space. Masai giraffes (Giraffa camelopardalis tippelskirchi) of Tanzania live in distinct social subpopulations that overlap spatially, enabling us to simultaneously explore environmental and social factors correlated with demographic variation in a metapopulation of >1,400 adult females and calves. We considered statistically distinct communities in the social network as subpopulations and tested for variation among the 10 subpopulations in adult female survival, calf survival, and reproductive rate (calf‐to‐adult female ratio). We then related variation in demographic rates among subpopulations to differences in vegetation, soil type, proximity to 2 types of human settlements, local giraffe population density, and social metrics of relationship strength and exclusivity among adult females. We did not find any among‐subpopulation effects on adult female survival, suggesting adult female survival is buffered against environmental heterogeneity among subpopulations. Variation in calf demographic rates among subpopulations were correlated with vegetation, soils, anthropogenic factors, and giraffe population density but not with adult female relationship metrics, despite substantial spatial overlap. Subpopulations with more dense bushlands in their ranges had lower calf survival probabilities, and those closer to human settlements had higher reproductive rates, possibly because of spatial gradients in natural predation. Reproductive rates were higher in subpopulations with more volcanic soils, and calf survival probabilities were greater in subpopulations with higher local adult female densities, possibly related to higher‐quality habitat associated with fertile soils or lower predation risk, or to greater competitive ability. The variation in fitness among subpopulations suggests that giraffes do not move unhindered among resource patches to equalize reproductive success, as expected according to an ideal free distribution. The differences in calf survival and reproductive rates could rather indicate intercommunity differences in competitive ability, perception, learning, or experience. Our approach of comparing demography among spatially overlapping yet distinct socially defined subpopulations provides a biologically meaningful way to quantify environmental and social factors influencing fine‐scale demographic variation for social species. published
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- 2021
15. Laboulbeniomycetes: Intimate Fungal Associates of Arthropods
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Donald H. Pfister, Meredith Blackwell, and Danny Haelewaters
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0106 biological sciences ,0301 basic medicine ,Laboulbeniales ,Biodiversity ,Mycology ,Population biology ,Hymenoptera ,Biology ,010603 evolutionary biology ,01 natural sciences ,Host-Parasite Interactions ,03 medical and health sciences ,Ascomycota ,Genus ,Animals ,Arthropods ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,fungi ,Laboulbeniomycetes ,030108 mycology & parasitology ,biology.organism_classification ,Evolutionary biology ,Insect Science ,Arthropod - Abstract
Arthropod–fungus interactions involving the Laboulbeniomycetes have been pondered for several hundred years. Early studies of Laboulbeniomycetes faced several uncertainties. Were they parasitic worms, red algal relatives, or fungi? If they were fungi, to which group did they belong? What was the nature of their interactions with their arthropod hosts? The historical misperceptions resulted from the extraordinary morphological features of these oddly constructed ectoparasitic fungi. More recently, molecular phylogenetic studies, in combination with a better understanding of life histories, have clearly placed these fungi among filamentous Ascomycota (subphylum Pezizomycotina). Species discovery and research on the classification of the group continue today as arthropods, and especially insects, are routinely collected and examined for the presence of Laboulbeniomycetes. Newly armed with molecular methods, mycologists are poisedto use Laboulbeniomycetes–insect associations as models for the study of a variety of basic evolutionary and ecological questions involving host–parasite relationships, modes of nutrient intake, population biology, host specificity, biological control, and invasion biology. Collaboration between mycologists and entomologists is essential to successfully advance knowledge of Laboulbeniomycetes and their intimate association with their hosts.
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- 2021
16. Reproducibility of hierarchical modeling analyses in ecology
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Kellner, Kenneth
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Population Biology ,Ecology and Evolutionary Biology ,Life Sciences - Abstract
Many journals now require authors to submit both code and data along with a publication. Several studies have shown that the proportion of these papers for which the shared code and data can be said to replicate the analysis is low, even with aid from the original authors. We plan a similar study of the ecology and wildlife conservation literature, specifically focusing on papers that estimate species distribution or abundance via hierarchical modeling.
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- 2022
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17. Movement and behavioural phenotypes: systematic review and meta-analysis protocols
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Martinig, April Robin, Lagisz, Malgorzata, Burk, Spenser, Yang, Yefeng, and Nakagawa, Shinichi
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Population Biology ,Evolution ,behavior ,Ecology and Evolutionary Biology ,Life Sciences ,Behavior and Ethology ,Social and Behavioral Sciences ,migration ,behaviour ,FOS: Psychology ,meta-analysis ,personality ,Personality and Social Contexts ,Psychology ,movement ,dispersal ,Biology - Abstract
This is a registration of a meta-analysis that will broadly address how dispersal and movement covary with behavioural phenotypes.
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- 2022
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18. Expression of Concern: Head Lice of Pygmies Reveal the Presence of Relapsing Fever Borreliae in the Republic of Congo
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Bacterial Diseases ,Arthropoda ,Epidemiology ,Disease Vectors ,Pathology and Laboratory Medicine ,Microbiology ,parasitic diseases ,Medicine and Health Sciences ,Genetics ,Animals ,skin and connective tissue diseases ,Microbial Pathogens ,Evolutionary Biology ,Bacteria ,Acinetobacter ,Population Biology ,Borrelia ,Head Lice ,Organisms ,Biology and Life Sciences ,Invertebrates ,Borrelia Infection ,Insect Vectors ,Bacterial Pathogens ,Insects ,Infectious Diseases ,Haplotypes ,Medical Microbiology ,Haplogroups ,Pathogens ,Lice ,Population Genetics ,Research Article ,Acinetobacter Infections ,Body Lice - Abstract
Background Head lice, Pediculus humanus capitis, occur in four divergent mitochondrial clades (A, B, C and D), each having particular geographical distributions. Recent studies suggest that head lice, as is the case of body lice, can act as a vector for louse-borne diseases. Therefore, understanding the genetic diversity of lice worldwide is of critical importance to our understanding of the risk of louse-borne diseases. Methodology/Principal Findings Here, we report the results of the first molecular screening of pygmies’ head lice in the Republic of Congo for seven pathogens and an analysis of lice mitochondrial clades. We developed two duplex clade-specific real-time PCRs and identified three major mitochondrial clades: A, C, and D indicating high diversity among the head lice studied. We identified the presence of a dangerous human pathogen, Borrelia recurrentis, the causative agent of relapsing fever, in ten clade A head lice, which was not reported in the Republic of Congo, and B. theileri in one head louse. The results also show widespread infection among head lice with several species of Acinetobacter. A. junii was the most prevalent, followed by A. ursingii, A. baumannii, A. johnsonii, A. schindleri, A. lwoffii, A. nosocomialis and A. towneri. Conclusions/Significance Our study is the first to show the presence of B. recurrentis in African pygmies’ head lice in the Republic of Congo. This study is also the first to report the presence of DNAs of B. theileri and several species of Acinetobacter in human head lice. Further studies are needed to determine whether the head lice can transmit these pathogenic bacteria from person to another., Author Summary Head lice, Pediculus capitis humanus, and body lice, Pediculus h. humanus, are obligatory ectoparasites that feed exclusively on human blood. Currently, the body louse is the only recognized vector of at least three deadly bacterial pathogens that have killed millions of peoples, namely: Rickettsia prowazekii, Bartonella quintana and Borrelia recurrentis, responsible for epidemic typhus, trench fever and relapsing fever, respectively. In this work, we aimed to study the genetic diversity of head lice collected from African Pygmies in the Republic of Congo and to look for louse-borne pathogens in these lice. We detected B. recurrentis in head lice belonged to clade A that is prevalent in the Republic of Congo. Our study also show, for the first time, the presence of DNAs of B. theileri and several species of Acinetobacter in human head lice. Despite several investigations into the transmissibility of numerous infectious agents, no conclusive evidence has demonstrated the transmission of disease by head lice. That said, we believe that pathogens detected in head lice may be an indirect tool for evaluating the risk of louse-borne diseases in humans.
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- 2022
19. Lifetime fitness effects of dispersal: systematic review and meta-analysis protocols
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Martinig, April Robin, Lagisz, Malgorzata, Burk, Spenser, Yang, Yefeng, and Nakagawa, Shinichi
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meta-analysis ,reproduction ,Population Biology ,Evolution ,Ecology and Evolutionary Biology ,Life Sciences ,Marine Biology ,movement ,dispersal ,migration ,Biology ,survival ,fitness - Abstract
This is a registration of a meta-analysis that will broadly address the short- and long-term fitness costs and benefits of dispersal.
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- 2022
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20. Phylogenomic assessment of the role of hybridization and introgression in trait evolution
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Luay Nakhleh, Zhen Cao, Huw A. Ogilvie, and Yaxuan Wang
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Evolutionary Genetics ,Gene Flow ,Cancer Research ,Computer and Information Sciences ,Evolutionary Processes ,Heredity ,Genetic Speciation ,Introgression ,Quantitative Trait Loci ,Biology ,QH426-470 ,Genetic Introgression ,Research and Analysis Methods ,Gene flow ,Evolution, Molecular ,Phylogenomics ,Genetics ,Evolutionary Systematics ,Molecular Biology ,Gene ,Hybridization ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Taxonomy ,Data Management ,Evolutionary Biology ,Biological data ,Models, Genetic ,Population Biology ,Simulation and Modeling ,Gene tree ,Computational Biology ,Biology and Life Sciences ,Phylogenetic Analysis ,Phylogenetics ,Tree (data structure) ,Phenotype ,Evolutionary biology ,Trait ,Population Genetics ,Research Article - Abstract
Trait evolution among a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a binary trait’s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis in the presence of gene flow could lead to misleading hypotheses about trait evolution., Author summary Traits include an organism’s appearance, form, structure, development, physiology, biochemistry and behaviour. They are subject to the same evolutionary processes as their associated genes, including convergence and incomplete lineage sorting. In the former case traits are gained or lost independently in different species, in the latter variation within ancestral species enables a present-day pattern of traits seemingly at odds with the tree of life. Advances in sequencing and new methods to reconstruct evolutionary history have made us increasingly aware of how between-species hybridization results in a network, not a tree, of life. To understand the impact of hybridization on trait evolution we introduce the concept of xenoplasy where present-day traits are shared with ancestral organisms through hybridization instead of strictly tree-like speciation. We have developed a measure called the global xenoplasy risk factor (G-XRF) to quantify the risk that xenoplasy has contributed to a present-day trait pattern, and demonstrate its effectiveness on real and simulated data.
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- 2021
21. The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection
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Enrique Santiago-Rubio, Armando Caballero, and Irene Novo
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Genetic Markers ,Cancer Research ,Heredity ,Evolutionary Processes ,Population Size ,Single Nucleotide Polymorphisms ,QH426-470 ,Polymorphism, Single Nucleotide ,Biochemistry ,Linkage Disequilibrium ,Human Genomics ,Population Metrics ,Effective Population Size ,Natural Selection ,Genetics ,Humans ,Selection, Genetic ,Molecular Biology ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Population Density ,Recombination, Genetic ,Evolutionary Biology ,Population Biology ,Nucleotides ,Chromosome Mapping ,Computational Biology ,Biology and Life Sciences ,Genomics ,Population Genetics ,Research Article - Abstract
The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Directional selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate, or they do it very weakly, with recombination rate, nucleotide diversity, proportion of polymorphic sites, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures mainly reflect demographic changes in population size across generations., Author summary The inference of the demographic history of populations is of great relevance in evolutionary biology. This inference can be made from genomic data using coalescence methods or linkage disequilibrium methods. However, the assessment of these methods is usually made assuming neutrality (absence of selection). Here we show by computer simulations and analyses of human data that the estimates of historical effective population size obtained from linkage disequilibrium between markers are virtually unaffected by natural selection, either positive or negative. In contrast, estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for recent estimations of human demography.
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- 2022
22. Data for the article 'Life-stage and sex influence Philornis ectoparasitism in a Neotropical woodpecker (Melanerpes striatus) with essential male parental care'
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LaPergola, Joshua B.
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Other Ecology and Evolutionary Biology ,Ornithology ,Population Biology ,Animal Sciences ,FOS: Biological sciences ,Ecology and Evolutionary Biology ,Laboratory and Basic Science Research Life Sciences ,Life Sciences ,Behavior and Ethology ,Biology ,Zoology - Abstract
Data for the article "Life-stage and sex influence Philornis ectoparasitism in a Neotropical woodpecker (Melanerpes striatus) with essential male parental care". The files contain data on the occurrence of Philornis parasitism in adult and nestling Hispaniolan Woodpeckers from a field site near Jarabacoa, La Vega, Dominican Republic.
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- 2022
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23. Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species
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Ayako Izuno, Yusuke Onoda, Gaku Amada, Keito Kobayashi, Mana Mukai, Yuji Isagi, Kentaro K. Shimizu, University of Zurich, and de Meaux, Juliette
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Gene Flow ,Cancer Research ,Topography ,Heredity ,Evolution ,Genetic Speciation ,Single Nucleotide Polymorphisms ,Myrtaceae ,Oceania ,QH426-470 ,Hawaii ,Homozygosity ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,Geographical Locations ,10127 Institute of Evolutionary Biology and Environmental Studies ,Behavior and Systematics ,Genetics ,Selection, Genetic ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Genetics (clinical) ,Islands ,Population Density ,Evolutionary Biology ,Landforms ,Ecology ,Population Biology ,Whole Genome Sequencing ,Altitude ,fungi ,Biology and Life Sciences ,Geomorphology ,Genomics ,United States ,Genetic Mapping ,Oxidative Stress ,Phenotype ,Haplotypes ,People and Places ,North America ,Genetic Polymorphism ,Earth Sciences ,570 Life sciences ,biology ,590 Animals (Zoology) ,Population Genetics ,Genome, Plant ,Research Article - Abstract
Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments. The continuous M. polymorpha forest stands on the island of Hawaii were differentiated into three genetic clusters, each of which grows in a distinctive environment and includes substantial genetic and phenotypic diversity. The three genetic clusters showed signatures of selection in genomic regions encompassing genes relevant to environmental adaptations, including genes associated with light utilization, oxidative stress, and leaf senescence, which are likely associated with the ecological differentiation of the species. Our demographic modeling suggested that the glaberrima cluster in wet environments maintained a relatively large population size and two clusters split: polymorpha in the subalpine zone and incana in dry and hot conditions. This ecological divergence possibly began before the species colonized the island of Hawaii. Interestingly, the three clusters recovered genetic connectivity coincidentally with a recent population bottleneck, in line with the weak reproductive isolation observed in the species. This study highlights that the degree of genetic differentiation between ecologically-diverged populations can vary depending on the strength of natural selection in the very early phases of speciation., Author summary Knowledge about how genetic barriers are formed between populations in distinct environments is valuable to understand the processes of speciation and conserve biodiversity. Metrosideros polymorpha, an endemic woody species in the Hawaiian Islands, is a good system to study developing genetic barriers in a species, because it colonized the diverse environments and diversified the morphology for a relatively short period of time. We analyzed the genomes of 70 M. polymorpha plants from a broad range of environments on the island of Hawaii to infer the current and past genetic barriers among them. Currently, M. polymorpha plants growing in different environments have substantially different genomes, especially at the genomic regions with genes putatively controlling physiology to fit in distinct environment. However, in its history, they had hybridized with one another, possibly because plants formerly growing in different environments came into close contact due to the climate changes. It is suggested that genetic barriers can easily strengthen or weaken depending on environments splitting the ecology of a species before reproductive isolation becomes complete.
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- 2022
24. The Avian Migrant: The Biology of Bird Migration
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Rappole, John, author and Rappole, John
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- 2013
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25. Biol 548T project
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SCHENK, SIOBHAN
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Population Biology ,metacommunity ,Ecology and Evolutionary Biology ,invertebrate ,Life Sciences ,rockpool - Abstract
This is for Biol 548. It analyzes the data from Jurek, Kolasa, 2022, "Long-term Rocky Tidal Community Data from Discovery Bay, Jamaica", https://doi.org/10.5683/SP3/FNAU9L, Borealis
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- 2022
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26. Effects of natural disturbances on forest soils
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Martin, Phil, Izquerdo, Leticia, Luyssaert, Sebastiaan, Guenet, Bertrand, Manzoni, Stefano, Spake, Rebecca, Santonja, Mathieu, and Yuste, Jorge
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Population Biology ,Terrestrial and Aquatic Ecology ,insect pests ,Ecology and Evolutionary Biology ,natural disturbances ,Life Sciences ,Biodiversity ,drought ,plant pathogens ,soil ecology ,windthrow ,Biology ,soil fauna ,fire - Abstract
This is a protocol for a systematic map of studies that have examined the impacts of natural disturbances on soil fauna in forest ecosystems. The systematic map aims to characterise these studies, identify opportunities for future quantitative synthesis, and identify knowledge gaps that warrant further primary studies.
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- 2022
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27. Effects of natural disturbances on soil fauna in forests: a systematic map protocol
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Martin, Phil, Izquerdo, Leticia, Luyssaert, Sebastiaan, Guenet, Bertrand, Manzoni, Stefano, Spake, Rebecca, Santonja, Mathieu, and Yuste, Jorge
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Population Biology ,Terrestrial and Aquatic Ecology ,insect pests ,Ecology and Evolutionary Biology ,natural disturbances ,Life Sciences ,Biodiversity ,drought ,plant pathogens ,soil ecology ,windthrow ,Biology ,soil fauna ,fire - Abstract
This is a protocol for a systematic map of studies that have examined the impacts of natural disturbances on soil fauna in forest ecosystems. The systematic map aims to characterise these studies, identify opportunities for future quantitative synthesis, and identify knowledge gaps that warrant further primary studies.
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- 2022
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28. Manuscript Registration: Asymptomatic Bordetella pertussis infections in a longitudinal cohort of young African infants and their mothers
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Gunning, C.
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Population Biology ,IS481 ,Epidemiology ,pertussis ,Respiratory Tract Diseases ,Ecology and Evolutionary Biology ,Life Sciences ,Zambia ,Diseases ,qPCR ,Maternal and Child Health ,Africa ,Medicine and Health Sciences ,Lusaka ,eLife ,Public Health - Abstract
Final data and code for manuscript by Gill & Gunning et al., eLife 2021.
- Published
- 2022
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29. Effects of soil type on body condition of an endemic and a widespread woodland salamander
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Marsh, David
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Population Biology ,FOS: Biological sciences ,Animal Sciences ,Ecology and Evolutionary Biology ,Life Sciences ,complex mixtures ,Zoology - Abstract
One of the central questions in ecology is why some species are common and others are rare. Eastern Redback salamanders (Plethodon cinereus) are one of the most common vertebrates in North America. In contrast, Big Levels Salamanders (Plethodon sherando) have one of the smallest ranges on any vertebrate in North America. Based on USGS soil maps, the range of Big Levels salamanders largely corresponds to an unusual soil type with low organic content, low pH, and high levels of some minerals (e.g. manganese). These soils are quite sandy and support an unusual plant community rather than the mature, deciduous forest in which salamanders are typically found. We hypothesize that Big Levels salamanders are specifically adapted to this soil type and will maintain higher body condition on their own soil type as compared to surrounding soil types, and similarly that Redback Salamanders will maintain higher body condition on their own soil type as compared to the Big Levels soil type. We will test this by measuring change in body condition (residuals of regression of body mass on SVL and tail length) of both species of salamanders in field enclosures containing one salamander of each species and either soil that is characteristic of Big Levels or soil from more typical areas where Eastern Redbacks are found.
- Published
- 2022
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- View/download PDF
30. Wits Face Database: Reliability of forensic facial identification from CCTV recordings with implications for admissibility to court
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Bacci, Nicholas, Davimes, Joshua, Steyn, Maryna, and Briers, Nanette
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Photo comparison ,Population Biology ,Image Processing ,Ecology and Evolutionary Biology ,Face -- Anatomy and Histology ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Research Methods in Life Sciences ,Life Sciences ,Vision Science ,Biological and Physical Anthropology ,facial photographs ,Social and Behavioral Sciences ,facial identification ,FOS: Sociology ,Image analysis ,facial recognition ,Engineering ,Anthropology ,Photography ,morphological analysis ,facial comparison ,CCTV ,MeSH Unique ID: D005145 ,Biomedical Engineering and Bioengineering ,Videorecording - Abstract
The human face is important in social, cultural and recognition contexts. Many research fields make use of faces to understand human interaction and identify individuals. Studies relying on facial image data often make use of ad hoc datasets specifically created for those studies as there is a dearth of large scale controlled and matching facial image databases. Actualistic (taken in a real life, natural setting) and standardised databases of facial images can be of extreme value to many research areas, such as facial identification and recognition. While multiple face databases are available, the majority, if not all, are developed in order to address very specific questions and hypotheses with limited standardisation, severely limiting their potential applicability. The Wits Face Database was developed as a generic, yet actualistic dataset of facial images obtained from consenting young adult South African male individuals. This database consists of high resolution standardised facial photographs (3264 x 4080 pixels) and corresponding closed-circuit television (CCTV) recordings of male South Africans under different camera conditions. A total of 6220 standardised (clothing and background controlled) and natural (visible clothing and out of focus background) facial photographs of 622 matching individuals in five different views are included. Corresponding CCTV footage of 334 of these individuals is also included. Across both the CCTV recordings and the photographs, the faces were captured in five different views: anterior, left 45-degree, left lateral, right 45-degree, and right lateral. The CCTV recordings were grouped under the following actualistic conditions: a standard internet protocol (IP) CCTV set-up, a low-resolution analogue CCTV set-up, an eye-level IP CCTV system, and the standard IP CCTV set-up with the addition of sunglasses and caps for target individuals. A detailed description of the composition and acquisition process of the database will be made available in a database descriptor publication format. The database is available strictly for non-commercial scientific research following approval of a formal application, assessed by the School of Anatomical Sciences’ Collections Committee within the University of the Witwatersrand. A total of 622 participants were photographed. Each participant had 10 photographs taken in different views and at two different distances (1.5m and 5m). The total number of unique photographs included in the database is 6220. All photographs were captured and stored both as native RAW and .jpeg formats. The effective duplication of photographs in these two formats results in 12440 images stored as part of the database. A total of 334 participants were also recorded using different CCTV cameras from the Wits Protection Services surveillance system. An approximate 30 seconds of footage was captured for each participant and extracted as .mp4 videos. The total approximate size of the database is 292 GB. Approximately 92 GB of the database consists of the CCTV footage with the remaining 200 GB being the photographs in all modes of capturing (5 views and two camera distances).
- Published
- 2022
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31. An explorative RNA-seq analysis of Antarctic fur seal mother-pup pairs from low and high density breeding populations
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Nagel, Rebecca, Stainfield, Claire, Toscani, Camille, Fox-Clarke, Cameron, Forcada, Jaume, and Hoffman, Joe
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Population Biology ,Animal Sciences ,Ecology and Evolutionary Biology ,Life Sciences ,Marine Biology ,Biology - Abstract
The interaction between an individual’s phenotype and its environment can provide insights into the origin and extent of local adaptation. Understanding how an individual may adapt and match its phenotype to a particular environment is therefore a key objective of molecular ecology. Here, we will use an RNA-sequencing approach to compare the blood mRNA levels of Antarctic fur seals from two colonies of contrasting population density (low and high) at two seasonal time points (shortly after birth and shortly before weaning). Samples were collected from mother-pup pairs during two subsequent breeding seasons (2018-19 and 2019-20) on the sub-Antarctic island of Bird Island, South Georgia. This is an exploratory study to better understand (a) how gene expression profiles differ among individuals experiencing low and high density conditions, (b) how gene expression profiles change throughout the season (from birth to weaning), (c) how gene expression profiles reflect differing pressures on mothers and pups, and (d) how gene expression profiles reflect inter-annual variation. This amounts to four key pair-wise comparisons in our differential gene expression design matrix (low vs high density, birth vs weaning, mother vs pup, 2018-19 vs 2019-20) and interaction terms thereof.
- Published
- 2022
- Full Text
- View/download PDF
32. Ecology and Genetics of Three Canadian Butterflies: An Intro
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Contursi, Michela M
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Other Ecology and Evolutionary Biology ,Rocky Mountain Apollo ,Population Biology ,Bog Copper ,Mottled Duskywing ,population dynamics ,Biodiversity ,molecular ecology ,Biology ,Molecular Biology - Abstract
Canadian butterflies are an iconic and well-loved group of insects. Understanding species ecological tendencies and genetic makeup is crucial for conservation and sustainability of butterfly populations on a large scale. Even having a brief overview of select butterfly species deepens one's appreciation for these small creatures. My USRI project focused on mark-recapture programs to study population dynamics and genetic sampling for the Mottled Duskywing, Bog Copper, and Rocky Mountain Apollo butterflies, as well as PCR testing for the presence of Wolbachia, an infectious bacteria, in Mottled Duskywing.
- Published
- 2022
33. A Theoretical Perspective on Parasite-Host Coevolution with Alternative Modes of Infection
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Shillcock, George N
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game theory ,adaptive dynamics ,Population Biology ,Evolution ,Virus Diseases ,infectious disease ,Ecology and Evolutionary Biology ,transmission ,Life Sciences ,Disease Modeling ,Nash equilibrium ,pathogen - Abstract
We investigate how natural selection shapes the coevolution of parasitism. We discuss the antagonism fuelled by parasites’ necessity to transmit to novel hosts, and host’s desire to minimise virulence. In support, we build a mathematical model which considers the epidemiology and life-history trade-offs faced by an obligate microparasite and its host. Our model allows parasites to be transmitted to new hosts via direct contact (horizontally) or from parent to offspring during birth (vertically). We test the hypothesis that vertical transmission causes virulence to diminish in the long run, and contrary to widely accepted views, find that vertical transmission need not result in benign coevolutionary outcomes in general. However, vertical transmission does promotes benign parasitism whenever: it is cheap for the host to retaliate; horizontal transmission saturates quickly; or the intrinsic growth rate of the host population is low.
- Published
- 2022
34. Population biology of a selfish sex ratio distorting element in a booklouse (Psocodea: Liposcelis )
- Author
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Steve J. Perlman and Christina N. Hodson
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Male ,0106 biological sciences ,0301 basic medicine ,food.ingredient ,Offspring ,Feminization (biology) ,Population ,Population biology ,Biology ,Neoptera ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,food ,Animals ,Sex Ratio ,education ,Ecology, Evolution, Behavior and Systematics ,education.field_of_study ,biology.organism_classification ,Fecundity ,030104 developmental biology ,Evolutionary biology ,Liposcelis ,Female ,Wolbachia ,Sex ratio - Abstract
Arthropods harbour a variety of selfish genetic elements that manipulate reproduction to be preferentially transmitted to future generations. A major ongoing question is to understand how these elements persist in nature. In this study, we examine the population dynamics of an unusual selfish sex ratio distorter in a recently discovered species of booklouse, Liposcelis sp. (Psocodea: Liposcelididae) to gain a better understanding of some of the factors that may affect the persistence of this element. Females that carry the selfish genetic element only ever produce daughters, although they are obligately sexual. These females also only transmit the maternal half of their genome. We performed a replicated population cage experiment, varying the initial frequency of females that harbour the selfish element, and following female frequencies for 20 months. The selfish genetic element persisted in all cages, often reaching very high (and thus severely female-biased) frequencies. Surprisingly, we also found that females that carry the selfish genetic element had much lower fitness than their nondistorter counterparts, with lower lifetime fecundity, slower development and a shorter egg-laying period. We suggest that differential fitness plays a role in the maintenance of the selfish genetic element in this species. We believe that the genetic system in this species, paternal genome elimination, which allows maternal control of offspring sex ratio, may also be important in the persistence of the selfish genetic element, highlighting the need to consider species with diverse ecologies and genetic systems when investigating the effects of sex ratio manipulators on host populations.
- Published
- 2019
35. Genetic diversity and population structure of the rockpool shrimp Palaemon elegans based on microsatellites: evidence for a cryptic species and differentiation across the Atlantic–Mediterranean transition
- Author
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Inés González-Castellano, Jorge González-López, Ana M. González-Tizón, and Andrés Martínez-Lage
- Subjects
0106 biological sciences ,0301 basic medicine ,Species complex ,Range (biology) ,Population genetics ,Population ,lcsh:Medicine ,Population biology ,Biology ,Mediterranean ,Palaemon elegans ,010603 evolutionary biology ,01 natural sciences ,Article ,Evolutionary genetics ,03 medical and health sciences ,Mediterranean Sea ,Animals ,Genetic variability ,education ,lcsh:Science ,Atlantic Ocean ,Genetic diversity ,education.field_of_study ,Multidisciplinary ,lcsh:R ,Microsatellite ,Genetic Variation ,Shrimp ,030104 developmental biology ,Biogeography ,Evolutionary biology ,Genetic structure ,Cryptic species ,Atlantic ,Genetic markers ,lcsh:Q ,Palaemonidae ,Molecular ecology ,Microsatellite Repeats - Abstract
The rockpool shrimp Palaemon elegans is an ecologically important crustacean species within the European coastline fauna. In the present study, genetic diversity and population structure and connectivity were assessed by examining 21 polymorphic microsatellite loci at 13 sampling sites located along the natural distribution range. All localities showed similar levels of genetic variability. Significant deficits of heterozygosity were recorded, most likely due to the presence of null alleles. Genetic structure analyses revealed two clearly genetically distinct groups within P. elegans but without following any geographical or oceanographic basis. Thus, our results provided nuclear evidence for the existence of a Mediterranean cryptic species within P. elegans, highlighting the need to revise its taxonomic status. Regarding P. elegans sensu stricto, population structuring was reported across the Atlantic–Mediterranean transition area, where the Almería-Orán Front restricts the gene flow between the Atlantic and the Mediterranean population. Moreover, while population connectivity was suggested between all Mediterranean localities, some substructure was found within the Atlantic group. Canary Islands exhibited a weak but significant genetic differentiation from all Atlantic mainland localities, consistent with the isolation-by-distance pattern detected throughout the Atlantic population. Overall, all these findings provided new insights into the population biology of P. elegans complex.
- Published
- 2020
36. When do factors promoting genetic diversity also promote population persistence? A demographic perspective on Gillespie’s SAS-CFF model
- Author
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Sebastian J. Schreiber
- Subjects
0106 biological sciences ,0301 basic medicine ,Population Dynamics ,Population ,Population biology ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Gene Frequency ,Genetic variation ,Population growth ,Allele ,education ,health care economics and organizations ,Ecology, Evolution, Behavior and Systematics ,Probability ,Population Density ,Stochastic Processes ,education.field_of_study ,Genetic diversity ,Extinction ,Genetic Variation ,Storage effect ,Genetics, Population ,030104 developmental biology ,Evolutionary biology - Abstract
Classical stochastic demography predicts that environmental stochasticity reduces population growth rates and, thereby, can increase extinction risk. In contrast, in a 1978 Theoretical Population Biology paper, Gillespie demonstrated with his stochastic additive scale and concave fitness function (SAS-CFF) model that environmental stochasticity can promote genetic diversity. Extending the SAS-CFF to account for demography, I examine the simultaneous effects of environmental stochasticity on genetic diversity and population persistence. Explicit expressions for the per-capita growth rates of rare alleles and the population at low-density are derived. Consistent with Gillespie’s analysis, if the log-fitness function is concave and allelic responses to the environment are not perfectly correlated, then per-capita growth rates of rare alleles are positive and genetic diversity is maintained in the sense of stochastic persistence i.e. allelic frequencies tend to stay away from zero almost-surely and in probability. Alternatively, if the log-fitness function is convex, then per-capita growth rates of rare alleles are negative and an allele asymptotically fixates with probability one. If the population’s low-density, per-capita growth rate is positive, then the population persists in the sense of stochastic persistence, else it goes asymptotically extinct with probability one. In contrast to per-capita growth rates of rare alleles, the population’s per-capita growth rate is a decreasing function of the concavity of the log-fitness function. Moreover, when the log-fitness function is concave, allelic diversity increases the population’s per-capita growth rate while decreasing the per-capita growth rate of rare alleles; when the log-fitness function is convex, environmental stochasticity decreases the per-capita growth rate of rare alleles, but increases the population’s per-capita growth rate. Collectively, these results (i) highlight how mechanisms promoting population persistence may be at odds with mechanisms promoting genetic diversity, and (ii) provide conditions under which population persistence relies on existing standing genetic variation.
- Published
- 2020
37. Rodenticide baiting black rats (
- Author
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Martin Cagnato, Mickaël Baumann, Nicolas Guillerault, David Ringler, and James C. Russell
- Subjects
0106 biological sciences ,Ecology ,media_common.quotation_subject ,Intertidal zone ,Context (language use) ,Population biology ,Management, Monitoring, Policy and Law ,Biology ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,010601 ecology ,Habitat ,Temperate climate ,Rodenticide ,Mangrove ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Context Mangroves and intertidal habitats have been identified as particularly challenging environments for bait application within both tropical and temperate environments, because bait applied to areas that are tidally inundated could degrade rapidly or become inaccessible to rats. Aims To determine rat density, ranging behaviour and probability of detection using different monitoring devices; additionally, to determine the availability (persistence, durability and uptake) of rodenticide baits within tidally inundated mangrove habitats. Methods The population biology of black rats (Rattus rattus) was studied in two contrasting mangrove habitats on Europa Island, and spatially explicit mark–recapture studies were performed to estimate densities and activity of rats. A series of bait availability trials was conducted to determine the durability of rodenticide baits on the ground and uptake in the canopy (‘bait bolas’). Key results Black rats were found to be abundant in mangrove, and despite daily tidal inundation, still maintained ranging behaviour consistent with rats in adjacent terrestrial habitats. Larger rodenticide bait blocks remained within tidally inundated habitat throughout tidal cycles and were available and remained palatable to rats for at least three consecutive nights, although strong bait competition occurred with crabs. Bait bolas were available in mangrove canopy exclusively to rats and consumption commenced on the first night. Conclusions The results provide evidence that mangrove habitats are an important habitat for rats, but the biology of rats in these habitats does not meaningfully differ from adjacent terrestrial habitats. With the use of larger rodenticide blocks, tidal inundation does not affect bait availability, but crabs remain a major competitor for these baits. Alternatively, the present study revealed that bait bolas limit bait access to rats alone. Development as an aerial eradication technology should be also recommended. Implications These results provide a proof of concept that eradication of rats from tidally inundated habitats such as mangrove should be possible with only small modifications to current best practice.
- Published
- 2021
38. Growth and population biology of the sand-bubbler crab Scopimera crabricauda Alcock 1900 (Brachyura: Dotillidae) from the Persian Gulf, Iran
- Author
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Vahid Malekzadeh, Ehsan Kamrani, Sana Sharifian, and Mohsen Safaie
- Subjects
0106 biological sciences ,biology ,010604 marine biology & hydrobiology ,Persian Gulf ,Dotillid crabs ,Intertidal zone ,Population biology ,biology.organism_classification ,Von Bertalanffy model ,010603 evolutionary biology ,01 natural sciences ,language.human_language ,Animal science ,QL1-991 ,Dotillidae ,language ,Carapace ,Quadrat ,Sand bubbler crab ,Zoology ,Sex ratio ,Sex ratios ,Persian - Abstract
Background Dotillid crabs are introduced as one common dwellers of sandy shores. We studied the ecology and growth of the sand bubbler crab Scopimera crabricauda Alcock, 1900, in the Persian Gulf, Iran. Crabs were sampled monthly by excavating nine quadrats at three intertidal levels during spring low tides from January 2016 to January 2017. Results Population data show unimodal size-frequency distributions in both sexes. The Von Bertalanffy function was calculated at CWt = 8.76 [1 − exp (− 0.56 (t + 0.39))], CWt = 7.90 [1 − exp (− 0.59 (t + 0.40))] and CWt = 9.35 [1 − exp (− 0.57 (t + 0.41))] for males, females, and both sexes, respectively. The life span appeared to be 5.35, 5.07, and 5.26 years for males, females, and both sexes, respectively. The cohorts were identified as two age continuous groups, with the mean model carapace width 5.39 and 7.11 mm for both sexes. The natural mortality (M) coefficients stood at 1.72 for males, 1.83 for females, and 1.76 years−1 for both sexes, respectively. The overall sex ratio (1:0.4) was significantly different from the expected 1:1 proportion with male-biased. Recruitment occurred with the highest number of annual pulse once a year during the summer. Conclusions The results, which show slow growth, emphasize the necessity of proper management for the survival of the stock of S. crabricauda on the Iranian coast of the Persian Gulf.
- Published
- 2021
39. <scp>CpG</scp> methylation frequency of <scp> TET2 </scp> , <scp> GRIA2 </scp> , and <scp> CDKN2A </scp> genes in the North Atlantic fin whale varies with age and between populations
- Author
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Gísli A. Víkingsson, Marta Riutort, Miguel A. Peinado, Alex Aguilar, Berta Martín, and Raquel García-Vernet
- Subjects
Fin ,biology ,Whale ,Population biology ,Aquatic Science ,Evolutionary biology ,CDKN2A ,biology.animal ,DNA methylation ,biology.protein ,Epigenetics ,GRIA2 ,Gene ,Ecology, Evolution, Behavior and Systematics - Published
- 2021
40. Observable variations in human sex ratio at birth
- Author
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Qi Chen, Yanan Long, Andrey Rzhetsky, and Henrik Larsson
- Subjects
Male ,0106 biological sciences ,Sexual Selection ,Population Dynamics ,Global Health ,01 natural sciences ,Geographical locations ,5. Gender equality ,Public health surveillance ,Natural Selection ,Medicine and Health Sciences ,Cluster Analysis ,Public and Occupational Health ,Biology (General) ,0303 health sciences ,education.field_of_study ,Ecology ,Water pollutants ,Pollution ,Regression ,3. Good health ,Europe ,Computational Theory and Mathematics ,Modeling and Simulation ,Sexual selection ,Regression Analysis ,Female ,Public Health ,Sex ratio ,Research Article ,Evolutionary Processes ,QH301-705.5 ,Population ,Biology ,010603 evolutionary biology ,Human sex ratio ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Swedish population ,Population Metrics ,Electronic health record ,Air Pollution ,Genetics ,Humans ,Sex Ratio ,European Union ,education ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Sweden ,Pollutant ,Evolutionary Biology ,Models, Statistical ,Population Biology ,business.industry ,Ecology and Environmental Sciences ,Water Pollution ,Infant, Newborn ,Biology and Life Sciences ,Neonates ,Computational Biology ,United States ,13. Climate action ,Agriculture ,North America ,People and places ,business ,Ibm watson ,Developmental Biology ,Demography - Abstract
The human sex ratio at birth (SRB), defined as the ratio between the number of newborn boys to the total number of newborns, is typically slightly greater than 1/2 (more boys than girls) and tends to vary across different geographical regions and time periods. In this large-scale study, we sought to validate previously-reported associations and test new hypotheses using statistical analysis of two very large datasets incorporating electronic medical records (EMRs). One of the datasets represents over half (∼ 150 million) of the US population for over 8 years (IBM Watson Health MarketScan insurance claims) while another covers the entire Swedish population (∼ 9 million) for over 30 years (the Swedish National Patient Register). After testing more than 100 hypotheses, we showed that neither dataset supported models in which the SRB changed seasonally or in response to variations in ambient temperature. However, increased levels of a diverse array of air and water pollutants, were associated with lower SRBs, including increased levels of industrial and agricultural activity, which served as proxies for water pollution. Moreover, some exogenous factors generally considered to be environmental toxins turned out to induce higher SRBs. Finally, we identified new factors with signals for either higher or lower SRBs. In all cases, the effect sizes were modest but highly statistically significant owing to the large sizes of the two datasets. We suggest that while it was unlikely that the associations have arisen from sex-specific selection mechanisms, they are still useful for the purpose of public health surveillance if they can be corroborated by empirical evidences., Author summary The human sex ratio at birth (SRB), usually slightly greater than 1/2, have been reported to vary in response to a wide array of exogenous factors. In the literature, many such factors have been posited to be associated with higher or lower SRBs, but the studies conducted so far have focused on no more than a few factors at a time and used far smaller datasets, thus prone to generating spurious correlations. We performed a series of statistical tests on 2 large, country-wide health datasets representing the United States and Sweden to investigate associations between putative exogenous factors and the SRB, and were able to validate a set of previously-reported associations while also discovering new signals. We propose to interpret these results simply as public health indicators awaiting further empirical confirmation rather than as implicated in (adaptive) sexual selection mechanisms.
- Published
- 2021
41. Blood groups of Neandertals and Denisova decrypted
- Author
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Andres Ruiz-Linares, Pierre Faux, Pascal Bailly, Caroline Costedoat, Jacques Chiaroni, Silvana Condemi, Stéphane Mazières, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), School of Life Sciences [Fudan University], Fudan University [Shanghai], Etablissement Français du Sang Provence-Alpes Côte-d'Azur et Corse (EFS), and Mazières, Stéphane
- Subjects
0301 basic medicine ,Neanderthal ,Hominids ,Heredity ,Physiology ,[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology ,Social Sciences ,Homozygosity ,0302 clinical medicine ,INDEL Mutation ,Medicine and Health Sciences ,Neanderthals ,education.field_of_study ,Multidisciplinary ,biology ,Fossils ,Paleogenetics ,Hominidae ,Body Fluids ,[SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology ,Genetic Mapping ,Blood ,Phenotype ,Blood Group Antigens ,Medicine ,Physical Anthropology ,Anatomy ,Research Article ,Genotype ,Science ,Population ,Variant Genotypes ,03 medical and health sciences ,Archaic Humans ,ABO blood group system ,biology.animal ,Paleoanthropology ,Genetic variation ,Genetics ,Hominins ,Animals ,Allele ,education ,Denisovan ,Alleles ,Evolutionary Biology ,Polymorphism, Genetic ,Population Biology ,Haplotype ,Biology and Life Sciences ,Paleontology ,Genetic Variation ,biology.organism_classification ,030104 developmental biology ,Haplotypes ,Evolutionary biology ,Genetic Loci ,Anthropology ,Earth Sciences ,Blood Groups ,030217 neurology & neurosurgery ,Population Genetics - Abstract
International audience; Red cell blood group systems are crucial for safe transfusion, transplantation, and pregnancy monitoring. In addition, blood groups have long been investigated to decipher the origin of human populations, migration, adaptation, and admixture. However, since the extensive use of DNA polymorphisms in Anthropology, blood groups have been relegated to their primary application, blood transfusion. The finer genomic mapping of some Neanderthal and Denisova individuals about modern humans has provided significant evidence on the evolutionary history of both archaic and modern humans. However, despite their medical and anthropological interest, little is known about blood groups in archaic populations. To better understand the origin, expansion and encounter with Homo sapiens, we reappraised the available high-quality sequences of three Neanderthals (Vindija 33.19, Chagyrskaya 8, Altai Neandertal) and one Denisovan (Denisova 3) for 11 genes of the 7 blood group systems that are routinely screened in transfusion: ABO including H/ Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, and Diego. We show that Neanderthals and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing viral gut infection and all Neanderthal shared RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to possible pregnancies with complications. Lastly, we connect the Neanderthal RHD allele to two present-day Aboriginal Australians and Papuan, suggesting that a segment of the archaic genome was introgressed in this gene in non-Eurasian populations before their expansion towards Oceania. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems remain effective anthropological markers.
- Published
- 2021
42. Intriguing effects of selection intensity on the evolution of prosocial behaviors
- Author
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Alex McAvoy, Andrew Rao, and Christoph Hauert
- Subjects
0106 biological sciences ,Social Cognition ,Computer science ,Social Sciences ,01 natural sciences ,Infographics ,0302 clinical medicine ,Natural Selection ,Econometrics ,Psychology ,Prisoner's Dilemma ,Biology (General) ,Data Management ,media_common ,0303 health sciences ,Natural selection ,Ecology ,Applied Mathematics ,Fecundity ,Computational Theory and Mathematics ,Prosocial behavior ,Modeling and Simulation ,Physical Sciences ,Games ,Graphs ,Game theory ,Research Article ,Computer and Information Sciences ,Evolutionary Processes ,Social Psychology ,QH301-705.5 ,media_common.quotation_subject ,010603 evolutionary biology ,Competition (biology) ,Evolution, Molecular ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Population Metrics ,Game Theory ,Genetic drift ,Genetics ,Selection, Genetic ,Evolutionary dynamics ,Molecular Biology ,Axiom ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,030304 developmental biology ,Balance (metaphysics) ,Evolutionary Biology ,Behavior ,Models, Genetic ,Population Biology ,Data Visualization ,Cognitive Psychology ,Biology and Life Sciences ,Prisoner's dilemma ,Altruistic Behavior ,Prosocial Behavior ,Video Games ,Cognitive Science ,Recreation ,Mathematics ,030217 neurology & neurosurgery ,Neuroscience - Abstract
In many models of evolving populations, genetic drift has an outsized role relative to natural selection, or vice versa. While there are many scenarios in which one of these two assumptions is reasonable, intermediate balances between these forces are also biologically relevant. In this study, we consider some natural axioms for modeling intermediate selection intensities, and we explore how to quantify the long-term evolutionary dynamics of such a process. To illustrate the sensitivity of evolutionary dynamics to drift and selection, we show that there can be a “sweet spot” for the balance of these two forces, with sufficient noise for rare mutants to become established and sufficient selection to spread. This balance allows prosocial traits to evolve in evolutionary models that were previously thought to be unconducive to the emergence and spread of altruistic behaviors. Furthermore, the effects of selection intensity on long-run evolutionary outcomes in these settings, such as when there is global competition for reproduction, can be highly non-monotonic. Although intermediate selection intensities (neither weak nor strong) are notoriously difficult to study analytically, they are often biologically relevant; and the results we report suggest that they can elicit novel and rich dynamics in the evolution of prosocial behaviors., Author summary Theoretical models of populations have been useful for assessing when and how traits spread, in large part because they are simple. Rather than being used to reproduce empirical data, these idealized models involve relatively few parameters and are utilized to gain a qualitative understanding of what promotes or suppresses a trait. For prosocial traits, which entail a cost to self to help another, one thing that mathematical models often suggest is that competition to reproduce must be localized, meaning an individual must be fitter than just a small subset of the population in order to produce an offspring. We show here that this finding is not robust. Such traits can indeed proliferate when there is global competition for reproduction, which we demonstrate by increasing the degree to which payoffs from games affect birth rates. Since this kind of “stronger selection” has also been observed empirically, we discuss how it is incorporated into theoretical models more broadly.
- Published
- 2021
43. Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow
- Author
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Brenton von Takach, Vicki A. Thomson, Jari Cornelis, Damian C. Lettoof, Marthe Monique Gagnon, Fabien Aubret, Philip W. Bateman, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
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0106 biological sciences ,Topography ,Heredity ,[SDV]Life Sciences [q-bio] ,Marine and Aquatic Sciences ,01 natural sciences ,Population genomics ,Effective population size ,Inbreeding depression ,Inbreeding ,Elapidae ,Reptile Genomics ,Islands ,0303 health sciences ,Ecosystem health ,education.field_of_study ,Heterozygosity ,Multidisciplinary ,Ecology ,Environmental Biomarkers ,biology ,Eukaryota ,Snakes ,Genomics ,Squamates ,Geography ,Vertebrates ,Medicine ,Research Article ,Freshwater Environments ,Conservation of Natural Resources ,Ecological Metrics ,Science ,Population ,010603 evolutionary biology ,03 medical and health sciences ,Genetic drift ,Genetics ,Animals ,education ,030304 developmental biology ,Landforms ,Evolutionary Biology ,Population Biology ,Tiger ,Ecology and Environmental Sciences ,Genetic Drift ,Notechis scutatus ,Organisms ,Biology and Life Sciences ,Reptiles ,Aquatic Environments ,Genetic Variation ,Geomorphology ,Species Diversity ,Western Australia ,15. Life on land ,biology.organism_classification ,Genetics, Population ,Animal Genomics ,Wetlands ,Amniotes ,Earth Sciences ,Zoology ,Population Genetics - Abstract
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.
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- 2021
44. Selective sorting of ancestral introgression in maize and teosinte along an elevational cline
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Graham Coop, M. Taylor Perkins, Jeffrey Ross-Ibarra, Erin Calfee, Anne Lorant, Daniel J. Gates, and Mauricio, Rodney
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Cancer Research ,Heredity ,Introgression ,Single Nucleotide Polymorphisms ,Plant Science ,QH426-470 ,Plant Genetics ,Gene flow ,Plant Genomics ,skin and connective tissue diseases ,Genetics (clinical) ,education.field_of_study ,Genome ,Eukaryota ,Chromosome Mapping ,Genomics ,Cline (biology) ,Plants ,Adaptation, Physiological ,Experimental Organism Systems ,Sympatric speciation ,Engineering and Technology ,Genome, Plant ,Research Article ,Biotechnology ,Gene Flow ,Evolutionary Processes ,Physiological ,Population ,Bioengineering ,Biology ,Research and Analysis Methods ,Zea mays ,Model Organisms ,Genetic ,Plant and Algal Models ,parasitic diseases ,Genetics ,Animals ,Domestic Animals ,Grasses ,Adaptation ,education ,Domestication ,Hybridization ,Mexico ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Local adaptation ,Hybrid ,Evolutionary Biology ,Population Biology ,Human Genome ,Organisms ,Biology and Life Sciences ,Plant ,Maize ,Haplotypes ,Genetic Loci ,Evolutionary biology ,Chromosome Inversion ,Animal Studies ,Hybridization, Genetic ,Plant Biotechnology ,Generic health relevance ,Zoology ,Population Genetics ,Developmental Biology - Abstract
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations., Author summary When species expand their ranges, new encounters with diverse wild relatives can introduce deleterious genetic variation, but may also accelerate the colonization of novel environments by providing ‘ready-made’ genetic adaptations. Maize today is a global staple, far exceeding the original ecological niche of its wild progenitor. We show that gene flow from highland-endemic wild mexicana facilitated maize’s range expansion from the valleys where it was domesticated to sites over 1500m in the mountains of Mexico. We find loci where mexicana ancestry has been repeatedly favored in highland maize populations. We also find loci (including a newly identified inversion) where mexicana ancestry increases steeply with elevation, providing evidence for adaptive trade-offs. We additionally demonstrate selection against mexicana ancestry, especially near domestication genes. We sampled mexicana growing alongside maize fields, yet find little evidence that introgression is recent or locally-sourced genomewide or at adaptive loci. Rather, the majority of mexicana ancestry was introduced into maize over 1000 generations ago, and subsequently diverged and was sorted by selection in individual populations. These results add to our understanding of the effects of introgression on range expansions and adaptation.
- Published
- 2021
45. Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila
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Jason Bertram
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Cancer Research ,Single Nucleotide Polymorphisms ,Binomials ,QH426-470 ,Polynomials ,Genome ,Divergence ,Gene Frequency ,Invertebrate Genomics ,Natural Selection ,Genetics (clinical) ,Natural selection ,Drosophila Melanogaster ,Selection coefficient ,Eukaryota ,Animal Models ,Genomics ,Insects ,Deletion Mutation ,Order (biology) ,Experimental Organism Systems ,Physical Sciences ,Drosophila ,Drosophila melanogaster ,Research Article ,Evolutionary Processes ,Arthropoda ,Single-nucleotide polymorphism ,Biology ,Research and Analysis Methods ,Polymorphism, Single Nucleotide ,Model Organisms ,Genetic drift ,Genetics ,Animals ,Selection, Genetic ,Molecular Biology ,Allele frequency ,Ecology, Evolution, Behavior and Systematics ,Alleles ,Selection (genetic algorithm) ,Evolutionary Biology ,Population Biology ,Genetic Drift ,Organisms ,Biology and Life Sciences ,biology.organism_classification ,Invertebrates ,Algebra ,Animal Genomics ,Genetic Loci ,Evolutionary biology ,Mutation ,Animal Studies ,Zoology ,Entomology ,Mathematics ,Population Genetics - Abstract
Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive—not negative—selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations., Author summary Natural selection is the process fundamentally driving evolutionary adaptation; yet the specifics of how natural selection molds the genome are contentious. A prevailing neutralist view holds that the evolution of most mutations is essentially random. Here, we develop new theory that looks past the stochasticity of individual mutations and instead analyzes the behavior of mutations across the genome as a collective. We find that selection has a strong non-random influence on most of the Drosophila genome over short timescales (tens of generations), including the bulk of mutations that are not themselves directly targeted by selection. We show that this likely involves ongoing positive selection.
- Published
- 2021
46. Evolutionarily stable strategies in stable and periodically fluctuating populations: The Rosenzweig-MacArthur predator-prey model
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Grunert, Katrin, Holden, Helge, Jakobsen, Espen R., and Stenseth, Nils Chr.
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0106 biological sciences ,Food Chain ,Dynamical systems theory ,Population ,Population Dynamics ,010603 evolutionary biology ,01 natural sciences ,Models, Biological ,Evolutionarily stable strategy ,Stability theory ,evolution ,Applied mathematics ,Animals ,Computer Simulation ,Limit (mathematics) ,education ,Ecosystem ,Mathematics ,education.field_of_study ,Multidisciplinary ,Population Biology ,limit cycles ,Applied Mathematics ,Computational Biology ,Biological Sciences ,dynamical systems ,Ecology and Evolutionary Biology ,Adaptation, Physiological ,Biological Evolution ,010601 ecology ,SI Correction ,Predatory Behavior ,Physical Sciences ,Limit point ,ecology ,Evolution strategy - Abstract
Significance Many evolutionary studies of ecological systems assume, explicitly or implicitly, ecologically stable population dynamics. Ecological analyses typically assume, on the other hand, no evolution. We study a model (using predator–prey dynamics as an example) combining ecology and evolution within the same framework. For this purpose, we use the evolutionarily stable strategies (ESSs) framework, emphasizing that evolutionary change, in general, will occur as a result of mutant strategies being able to invade a population. The significance of our contribution is to derive mathematical conditions for the existence of an ESS in a periodically limit-cycle ecological system., An evolutionarily stable strategy (ESS) is an evolutionary strategy that, if adapted by a population, cannot be invaded by any deviating (mutant) strategy. The concept of ESS has been extensively studied and widely applied in ecology and evolutionary biology [M. Smith, On Evolution (1972)] but typically on the assumption that the system is ecologically stable. With reference to a Rosenzweig–MacArthur predator–prey model [M. Rosenzweig, R. MacArthur, Am. Nat. 97, 209–223 (1963)], we derive the mathematical conditions for the existence of an ESS when the ecological dynamics have asymptotically stable limit points as well as limit cycles. By extending the framework of Reed and Stenseth [J. Reed, N. C. Stenseth, J. Theoret. Biol. 108, 491–508 (1984)], we find that ESSs occur at values of the evolutionary strategies that are local optima of certain functions of the model parameters. These functions are identified and shown to have a similar form for both stable and fluctuating populations. We illustrate these results with a concrete example.
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- 2021
47. Aggregative cycles evolve as a solution to conflicts in social investment
- Author
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Silvia De Monte, Leonardo Miele, Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Evolutionary Biology, Max-Planck-Gesellschaft, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris
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0106 biological sciences ,0301 basic medicine ,Life Cycles ,Dictyosteliomycota ,[SDV]Life Sciences [q-bio] ,Evolutionary stability ,Population Dynamics ,Pathology and Laboratory Medicine ,01 natural sciences ,Systems Science ,Cell Movement ,Resource Acquisition Is Initialization ,Economics ,Medicine and Health Sciences ,Dictyostelium ,Evolutionary Emergence ,Biology (General) ,Cell Aggregation ,Ecology ,Dictyostelium Discoideum ,Eukaryota ,Protists ,Investment (macroeconomics) ,Biological Evolution ,Dynamical Systems ,Cell Motility ,Computational Theory and Mathematics ,Experimental Organism Systems ,Slime Molds ,Modeling and Simulation ,Physical Sciences ,Pathogens ,Research Article ,Pathogen Motility ,Cell type ,Computer and Information Sciences ,Evolutionary Processes ,Virulence Factors ,QH301-705.5 ,Motility ,Research and Analysis Methods ,010603 evolutionary biology ,Models, Biological ,Microbiology ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Model Organisms ,Genetics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Conflict escalation ,Evolutionary Biology ,Population Biology ,Protozoan Models ,Organisms ,Computational Biology ,Biology and Life Sciences ,Cell Biology ,Organismal Evolution ,Multicellular organism ,030104 developmental biology ,Microbial Evolution ,Animal Studies ,Biological dispersal ,Economic system ,Mathematics ,Developmental Biology - Abstract
Multicellular organization is particularly vulnerable to conflicts between different cell types when the body forms from initially isolated cells, as in aggregative multicellular microbes. Like other functions of the multicellular phase, coordinated collective movement can be undermined by conflicts between cells that spend energy in fuelling motion and ‘cheaters’ that get carried along. The evolutionary stability of collective behaviours against such conflicts is typically addressed in populations that undergo extrinsically imposed phases of aggregation and dispersal. Here, via a shift in perspective, we propose that aggregative multicellular cycles may have emerged as a way to temporally compartmentalize social conflicts. Through an eco-evolutionary mathematical model that accounts for individual and collective strategies of resource acquisition, we address regimes where different motility types coexist. Particularly interesting is the oscillatory regime that, similarly to life cycles of aggregative multicellular organisms, alternates on the timescale of several cell generations phases of prevalent solitary living and starvation-triggered aggregation. Crucially, such self-organized oscillations emerge as a result of evolution of cell traits associated to conflict escalation within multicellular aggregates., Author summary In aggregative multicellular life cycles, cells come together in heterogenous aggregates, whose collective function benefits all the constituent cells. Current explanations for the evolutionary stability of such organization presume that alternating phases of aggregation and dispersal are already in place. Here we propose that, instead of being externally driven, the temporal arrangement of aggregative life cycles may emerge from the interplay between ecology and evolution in populations with differential motility. In our model, cell motility underpins group formation and allows cells to forage individually and collectively. Notably, slower cells can exploit the propulsion by faster cells within multicellular groups. When the level of such exploitation is let evolve, increasing social conflicts are associated to the evolutionary emergence of self-sustained oscillations. Akin to aggregative life cycles, resource exhaustion triggers group formation, whereas conflicts within multicellular groups restrain resource consumption, thus paving the way for the subsequent unicellular phase. The evolutionary transition from equilibrium coexistence to life cycles solves conflicts among heterogenous cell types by integrating them on a timescale longer than cell division, that comes to be associated to multicellular organization.
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- 2021
48. Drivers of linkage disequilibrium across a species' geographic range
- Author
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Yvonne Willi and Kay Lucek
- Subjects
0106 biological sciences ,Cancer Research ,Linkage disequilibrium ,Heredity ,Range (biology) ,Single Nucleotide Polymorphisms ,Arabidopsis ,Plant Science ,QH426-470 ,Plant Genetics ,01 natural sciences ,Linkage Disequilibrium ,Plant Genomics ,Drosophila Proteins ,Genetics (clinical) ,Recombination, Genetic ,0303 health sciences ,biology ,Eukaryota ,Genomics ,Plants ,Biological Evolution ,Phylogeography ,Experimental Organism Systems ,Engineering and Technology ,Genome, Plant ,Research Article ,Biotechnology ,Evolutionary Processes ,Arabidopsis Thaliana ,Bioengineering ,Locus (genetics) ,Outcrossing ,Brassica ,Research and Analysis Methods ,Polymorphism, Single Nucleotide ,010603 evolutionary biology ,03 medical and health sciences ,Model Organisms ,Genetic drift ,Plant and Algal Models ,Genetics ,Molecular Biology ,Arabidopsis lyrata ,Alleles ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Evolutionary Biology ,Population Biology ,Genetic Drift ,Organisms ,Genetic Variation ,Biology and Life Sciences ,Selfing ,Mating system ,biology.organism_classification ,Genetic Loci ,Evolutionary biology ,Animal Studies ,Plant Biotechnology ,Population Genetics - Abstract
While linkage disequilibrium (LD) is an important parameter in genetics and evolutionary biology, the drivers of LD remain elusive. Using whole-genome sequences from across a species’ range, we assessed the impact of demographic history and mating system on LD. Both range expansion and a shift from outcrossing to selfing in North American Arabidopsis lyrata were associated with increased average genome-wide LD. Our results indicate that range expansion increases short-distance LD at the farthest range edges by about the same amount as a shift to selfing. However, the extent over which LD in genic regions unfolds was shorter for range expansion compared to selfing. Linkage among putatively neutral variants and between neutral and deleterious variants increased to a similar degree with range expansion, providing support that genome-wide LD was positively associated with mutational load. As a consequence, LD combined with mutational load may decelerate range expansions and set range limits. Finally, a small number of genes were identified as LD outliers, suggesting that they experience selection by either of the two demographic processes. These included genes involved in flowering and photoperiod for range expansion, and the self-incompatibility locus for mating system., Author summary Nearby genomic variants are often co-inherited because of limited recombination. The extent of non-random association of alleles at different loci is called linkage disequilibrium (LD) and is commonly used in genomic analyses, for example to detect regions under selection or to determine effective population size. Here we reversed testing and addressed how demographic history may affect LD within a species. Using genomic data from more than a thousand individuals of North American Arabidopsis lyrata from across the entire species’ range, we quantified the effect of postglacial range expansion and a shift in mating system from outcrossing to selfing on LD. We show that both factors lead to increased LD, and that the maximal effect of range expansion is comparable with a shift in mating system to selfing. Heightened LD involves deleterious mutations, and therefore, LD can also serve as an indicator of mutation accumulation. Furthermore, we provide evidence that some genes experienced stronger increases in LD possibly due to selection associated with the two demographic changes. Our results provide a novel and broad view on the evolutionary factors shaping LD that may also apply to the very many species that underwent postglacial range expansion.
- Published
- 2021
- Full Text
- View/download PDF
49. Expression of Concern: A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin
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Climatology ,Evolutionary Biology ,Atmospheric Science ,Heredity ,Heterozygosity ,Population Biology ,Geography ,Climate Change ,Ecology and Environmental Sciences ,Biology and Life Sciences ,Paleontology ,Phylogeography ,Biogeography ,Genetic Loci ,Genetics ,Earth Sciences ,Paleoclimatology ,Paleogenetics ,Population Genetics ,Alleles ,Research Article - Abstract
The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently—more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea daffodil especially during LGM because of strong variation in coastline caused by glaciations.
- Published
- 2022
50. RETURN URBANIZATION – THE LAST CHANCE FOR ENDANGERED SPECIES OF BIRDS IN EUROPE AND OTHERS HIGH-URBANISED REGIONS, OR IS IT?
- Author
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V. S. Friedmann, G. S. Eryomkin, and N. Yu. Zakharova
- Subjects
ornithology ,urbanization ,ethology ,population biology ,rare species ,conservation biology ,biodiversity ,urban ecology ,microevolution ,evolutionary biology ,rapid adaptation ,environmental stress ,Ecology ,QH540-549.5 - Abstract
We have demonstrated the universal nature of “recurrence urbanization” with the example of the interaction of the avifauna of the center of Nonblack Soil Zone with urban landscape. Wild birds are adapting to a sustainable livelihood in «island landscape». This process occurs for many rare and endangered species of birds, traditionally attributed to urbofoba (including middle spotted woodpecker, black stork, woodpigeon and large birds of prey, which are considered as unable to this). This process changes the original biological characteristics of species such as stenotopic, territorial conservatism, attachment to large tracts of undisturbed habitat to the opposite characteristics – insensitivity to the “island effect”, an active adaptation to life in microfragments of the original habitat type. As a result, the species of birds, which yesterday were urbofoba, begins to nest in urbanized “core” of the region, starting with “islands” of natural landscapes within it, and then in buildings. During the process of urbanization, these fragments turn increasingly altered as compared to the “mainland”, more isolated from it. Permissible nesting habitats are starting to include “islands” decreasing in area. We have shown that the population of different species during such “recurrence urbanization” changes uniformly. This change is provided by the restructuring of space-ethological structure under the “pressure” of environmental stress in the direction of greater labilization relations in the system. The behavior of individuals (flight distance, attitude to people and technology, atypical forms of feeding and placing nests) is changed only later, often much later than the beginning of urbanization. We have shown that what is happening can be described by par forсe model of quick adaptation proposed by V. V. Suslov. However, amendments are necessery to the connectivity of individuals in a population system, their sorting, directed along a gradient of urbanization, a special adaptation not only to environmental stress, but their variable relationships within the system – biotopical, spatial, social. We need to adjust the models of “island biogeography” in relation to “the islands” created by anthropogenic habitat fragmentation. After reaching equilibrium, postulated by standard models, recolonization of species on the “archipelago” begins to exceed extinction. After a period of latency L (proportional to the degree of conservatism for initial vital strategy of species (1)), and if the latter does not die out in the region for L years of retreat to the periphery under the “pressure” of urbanized “core”, the species undergo “recurrence urbanization”. “Recurrence urbanization” gives a chance to save rare and endangered species of birds in the earlier developed regions of Europe, European Russia and other regions of the globe. If appropriate species in the development of urbanization (with its consequence – the fragmentation of habitats far around the burgeoning “urbanized core”) could only retreat preserved in large tracts of intact natural communities, they were doomed to be guaranteed even if the timely capture of their custody. The number of intact arrays is always too short, their “islands” are too isolated from each other and are insufficient in size to maintain viable populations of the species concerned. Even with the full protected mode vulnerable species have a high probability of becoming extinct due to the island effect. The only salvation for these species is “recurrence urbanization” which allows them to exist stably not only on the mainland, but also in the “archipelago” of fragmented habitat, which is typologically similar to the mainland, to settle them back and increase the number. Possible ending of this process is complete urbanization and the rapid settlement of the region from the periphery back to the “urbanized core” (and even inside it). Even the first steps in this direction extremely promote the welfare of the species, and give the opportunity to reverse the adverse trend of population dynamics, to increase the stability of the species in the region. This is particularly important because converted landscape of earlier developed regions dramatically increases the instability of populations even for common birds. Fortunately, even the most vulnerable species of birds (due to ecological specialization and rigid attachment to the “favorite” habitats / territories) were not rigid, as it was previously thought. They adapt to anthropogenic landscape in exactly the same way as the others, but they start doing it later, so they make huge losses. This is the way in which they can be saved and are already beginning to flee. It is necessary to form the urban landscape and settlement structure in the region so as to facilitate the natural ongoing process, not hinder it. Factors of attractiveness for urban landscape / fragmented habitats for the “wild” species of birds are known, and the problem of people, urban economy is not to increase the risks.
- Published
- 2016
- Full Text
- View/download PDF
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