scholarly journals Modularity of genes involved in local adaptation to climate despite physical linkage

2017 ◽  
Author(s):  
Katie E. Lotterhos ◽  
Sam Yeaman ◽  
Jon Degner ◽  
Sally Aitken ◽  
Kathryn A. Hodgins
Keyword(s):  
Candidate Genes ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Pinus Contorta ◽  
Regulatory Networks ◽  
Pleiotropic Effects ◽  
Recombination Rates ◽  
Selection Pressures ◽  
Physical Linkage ◽  
Peer Community

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100050)BackgroundLinkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favoured for alleles with similar pleiotropic effects, with increased recombination favoured among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the genetic architecture of local adaptation to climate in lodgepole pine (Pinus contorta), based on associations with environments.ResultsWe identified many clusters of candidate genes and SNPs associated with distinct environments (aspects of aridity, freezing, etc.), and discovered low recombination rates among some candidate genes in different clusters. Only a few genes contained SNPs with effects on more than one distinct aspect of climate. There was limited correspondence between co-association networks and gene regulatory networks. We further showed how associations with environmental principal components can lead to misinterpretation. Finally, simulations illustrated both benefits and caveats of co-association networks.ConclusionsOur results supported the prediction that different selection pressures favored the evolution of distinct groups of genes, each associating with a different aspect of climate. But our results went against the prediction that loci experiencing different sources of selection would have high recombination among them. These results give new insight into evolutionary debates about the extent of modularity, pleiotropy, and linkage in the evolution of genetic architectures.

scholarly journals Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection

2017 ◽  
Author(s):  
Diala Abu Awad ◽  
Denis Roze
Keyword(s):  
Inbreeding Depression ◽  
Evolutionary Biology ◽  
Genetic Variance ◽  
Stabilizing Selection ◽  
Genetic Associations ◽  
Mutation Load ◽  
Recombination Rates ◽  
Self Fertilization ◽  
Selected Traits ◽  
Peer Community

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100041).The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic variance Vg, mutation load L and inbreeding depression δ under stabilizing selection acting on a arbitrary number n of quantitative traits coded by biallelic loci with additive effects. Overall, our model predicts a decrease in the equilibrium genetic variance with increasing selfing rates; however, the relationship between self-fertilization and the variables of interest depends on the strength of associations between loci, and three different regimes are observed. When the U/n ratio is low (where U is the total haploid mutation rate on selected traits) and effective recombination rates are sufficiently high, genetic associations between loci are negligible and the genetic variance, mutation load and inbreeding depression are well predicted by approximations based on single-locus models. For higher values of U/n and/or lower effective recombination, moderate genetic associations generated by epistasis tend to increase Vg, L and δ, this regime being well predicted by approximations including the effects of pairwise associations between loci. For yet higher values of U/n and/or lower effective recombination, a different regime is reached under which the maintenance of coadapted gene complexes reduces Vg, L and δ. Simulations indicate that the values of Vg, L and δ are little affected by assumptions regarding the number of possible alleles per locus.

Homology, Genes, and Evolutionary Innovation

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Biological Diversity ◽  
Cell Types ◽  
Origin And Evolution ◽  
Major Transitions ◽  
Form And Function ◽  
Historical Continuity ◽  
Evolutionary Innovation ◽  
Character Identity

Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This book provides the first mechanistically based theory of what homology is and how it arises in evolution. The book argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. It shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, the book applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, this book reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

scholarly journals Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Camilla A Santos ◽  
Gabriel G Sonoda ◽  
Thainá Cortez ◽  
Luiz L Coutinho ◽  
Sónia C S Andrade
Keyword(s):  
Local Adaptation ◽  
Differentially Expressed Genes ◽  
Evolutionary Biology ◽  
Rocky Shore ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Marine Species ◽  
Differentially Expressed ◽  
Planktonic Larva ◽  
Structure Changes

Abstract Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.

scholarly journals Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing

2021 ◽  
Author(s):  
Zhibin Li ◽  
chengcheng Sun ◽  
Fei Wang ◽  
Xiran Wang ◽  
Jiacheng Zhu ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Cell Types ◽  
Genetic Regulatory Networks ◽  
Peripheral Blood Mononuclear

Background: Immune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited. Methods: In this study, we compared the single-cell transcriptomes of 77 957 immune cells from 12 species using single-cell RNA-sequencing (scRNA-seq). Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells. Results: The results revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular cross-talks and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM-CD44 was highly conserved among the immune cells. Conclusions: This study is the first to provide a comprehensive analysis of the cross-species single-cell atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders

scholarly journals Molecular Evolution of Calcium Signaling and Transport in Plant Adaptation to Abiotic Stress

2021 ◽  
Vol 22 (22) ◽  
pp. 12308
Author(s):  
Tao Tong ◽  
Qi Li ◽  
Wei Jiang ◽  
Guang Chen ◽  
Dawei Xue ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Calcium Signaling ◽  
Stress Responses ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Cascade Reactions ◽  
Future Research ◽  
Spatiotemporal Pattern ◽  
Green Plants ◽  
Signaling Components

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca2+) signaling is characterized by the spatiotemporal pattern of Ca2+ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca2+ signaling remains elusive in green plants. We review mechanisms of Ca2+ membrane transporters and intracellular Ca2+ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca2+ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca2+ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca2+ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca2+ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

scholarly journals Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen

2017 ◽  
Author(s):  
Norfarhan Mohd-Assaad ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Local Adaptation ◽  
Cellular Localization ◽  
Plant Pathogens ◽  
Protein Transport ◽  
Selective Sweep ◽  
Abiotic Factors ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Evolutionary Trajectory ◽  
Selection Pressures

AbstractThe coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect a specific host. Hence, heterogeneity in the host genotypes and abiotic factors leads to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. We analyzed global field populations of Rhynchosporium commune, the pathogen causing barley scald disease, to identify candidate genes for local adaptation. Whole genome sequencing data generated for 125 isolates showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded proteins with functions related to both biotic and abiotic stresses. We found that selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.

COMPLEXITY OF THE SEARCH SPACE IN A MODEL OF ARTIFICIAL EVOLUTION OF GENE REGULATORY NETWORKS CONTROLLING 3D MULTICELLULAR MORPHOGENESIS

2009 ◽  
Vol 12 (03) ◽  
pp. 347-369 ◽  
Author(s):  
MICHAŁ JOACHIMCZAK ◽  
BORYS WRÓBEL
Keyword(s):  
Cell Fate ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Dimensional Space ◽  
Evolutionary Process ◽  
Search Space ◽  
Evolutionary Search ◽  
Genetic Operators ◽  
Genetic Elements ◽  
Gene Regulatory

The question of what properties of biological systems allow for efficient evolutionary search in complex fitness landscapes (evolvability) is one of the central interests both for the research in the field of evolutionary biology and artificial life. Here, we attempt to address this issue by using a model of 3D multicellular development in which cell fate is determined by differential gene expression in each cell. In our model, cells can vary in size and can move freely in 3D space, affected by forces of adhesion and repulsion. The development relies on an indirect mapping between the genotype and the morphology (the phenotype). Cell differentiation is allowed by positional information provided by diffusible factors. The state of the gene regulatory network (GRN) coded by the genome determines the cell fate (such as division, death, growth). The genetic elements in our systems define points in N-dimensional space. The connectivity in the GRN is determined by the proximity of these points; one can imagine the evolutionary process as their movement in space. Changing the number of dimensions of this space allows to ask directly the questions about the effect of the complexity of the search space on the efficiency of the evolutionary search. Higher dimensionality results in a larger search space, but in our model this search space can still be explored thanks to the action of genetic operators that allow for duplications of genetic elements, a mutational mechanism that allows for regulatory innovations in the network.

scholarly journals Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017 ◽  
Vol 49 (1) ◽  
Author(s):  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Maria T. Sardina ◽  
Gianluca Sottile ◽  
Anna M. Sutera ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Local Adaptation ◽  
Potential Candidate ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

2020 ◽  
Author(s):  
Tao Jiang ◽  
Meide Zhang ◽  
Chunxiu Wen ◽  
Xiaoliang Xie ◽  
Wei Tian ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Salvia Miltiorrhiza ◽  
Flower Color ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Anthocyanin Content ◽  
Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

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