In the presence of population structure: From genomics to candidate genes underlying local adaptation

AbstractUnderstanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. Mixed linear mrsodels that identify allele associations to environment, while controlling for genome-wide variation at other loci, have emerged as the method of choice when studying local adaptation. Despite their importance, it is unclear whether this approach performs better than identifying environmentally-associated SNPs without accounting for population structure. To examine this, we first use the mixed linear model GEMMA, and simple Spearman correlations, to identify SNPs showing significant associations to climate with and without accounting for population structure. Subsequently, using Italy and Sweden populations, we compare evidence of allele frequency differentiation (FST), linkage disequilibrium (LD), fitness variation, and functional constraint, underlying these SNPs. Using a lenient cut-off for significance, we find that SNPs identified by both approaches, and SNPs uniquely identified by Spearman correlations, were enriched at sites showing genomic evidence of local adaptation and function but were limited across Quantitative Trait Loci (QTL) explaining fitness variation. SNPs uniquely identified by GEMMA, showed no direct or indirect evidence of local adaptation, and no enrichment along putative functional sites. Finally, SNPs that showed significantly high FST and LD, were enriched along fitness QTL peaks and cis-regulatory/nonsynonymous sites showing significant functional constraint. Using these SNPs, we identify genes underlying fitness QTL, and genes linking flowering time to local adaptation. These include a regulator of abscisic-acid (FLDH) and flowering time genes PIF3, FIO1, and COL5.

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Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

BMC Plant Biology ◽

10.1186/s12870-021-03075-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yong Li ◽

Long-Chen Shi ◽

Nan-Cai Pei ◽

Samuel A. Cushman ◽

Yu-Tao Si

Keyword(s):

Drought Stress ◽

Differential Expression ◽

Local Adaptation ◽

Evolutionary Biology ◽

Molecular Ecology ◽

Evolutionary Process ◽

Reduction Process ◽

Heterogeneous Environments ◽

Significant Differential Expression ◽

Genetic Mechanisms

Abstract Background Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. Results Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation–reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. Conclusions Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

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The WZA: A window-based method for characterizing genotype-environment association

10.22541/au.162836421.16815307/v1 ◽

2021 ◽

Author(s):

Tom Booker ◽

Sam Yeaman ◽

Michael Whitlock

Keyword(s):

Population Structure ◽

Local Adaptation ◽

Selection Pressure ◽

Genetic Basis ◽

Natural Populations ◽

Original Study ◽

Published Data ◽

Heterogeneous Environments ◽

Candidate Loci ◽

Number Of Individuals

Genotype environment association (GEA) studies have the potential to elucidate the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the weighted-Z analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST. We analyze simulations modelling local adaptation to heterogeneous environments either using a GEA method that controls for population structure or an uncorrected approach. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. The WZA outperformed individual SNP approaches when the measured environment is not perfectly correlated with the true selection pressure or when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine and identified candidate loci that were not found in the original study.

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The WZA: A window-based method for characterizing genotype-environment association

10.1101/2021.06.25.449972 ◽

2021 ◽

Author(s):

Tom R Booker ◽

Sam Yeaman ◽

Michael Whitlock

Keyword(s):

Population Structure ◽

Local Adaptation ◽

Selection Pressure ◽

Genetic Basis ◽

Natural Populations ◽

Original Study ◽

Published Data ◽

Heterogeneous Environments ◽

Candidate Loci ◽

Number Of Individuals

Genotype environment association (GEA) studies have the potential to elucidate the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the weighted-Z analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST. We analyze simulations modelling local adaptation to heterogeneous environments either using a GEA method that controls for population structure or an uncorrected approach. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. The WZA outperformed individual SNP approaches when the measured environment is not perfectly correlated with the true selection pressure or when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine identified candidate loci that were not found in the original study.

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

Genome Biology and Evolution ◽

10.1093/gbe/evab050 ◽

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.

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Further twists in gastropod shell evolution

Biology Letters ◽

10.1098/rsbl.2007.0602 ◽

2008 ◽

Vol 4 (2) ◽

pp. 179-182 ◽

Cited By ~ 14

Author(s):

Reuben Clements ◽

Thor-Seng Liew ◽

Jaap Jan Vermeulen ◽

Menno Schilthuizen

Keyword(s):

Evolutionary Biology ◽

Logarithmic Spiral ◽

Spiral Growth ◽

Evolutionary Perspective ◽

Gastropod Shell ◽

Form And Function ◽

Evolutionary Origins ◽

Taxonomic Groups ◽

And Function ◽

Shell Coiling

The manner in which a gastropod shell coils has long intrigued laypersons and scientists alike. In evolutionary biology, gastropod shells are among the best-studied palaeontological and neontological objects. A gastropod shell generally exhibits logarithmic spiral growth, right-handedness and coils tightly around a single axis. Atypical shell-coiling patterns (e.g. sinistroid growth, uncoiled whorls and multiple coiling axes), however, continue to be uncovered in nature. Here, we report another coiling strategy that is not only puzzling from an evolutionary perspective, but also hitherto unknown among shelled gastropods. The terrestrial gastropod Opisthostoma vermiculum sp. nov. generates a shell with: (i) four discernable coiling axes, (ii) body whorls that thrice detach and twice reattach to preceding whorls without any reference support, and (iii) detached whorls that coil around three secondary axes in addition to their primary teleoconch axis. As the coiling strategies of individuals were found to be generally consistent throughout, this species appears to possess an unorthodox but rigorously defined set of developmental instructions. Although the evolutionary origins of O. vermiculum and its shell's functional significance can be elucidated only once fossil intermediates and live individuals are found, its bewildering morphology suggests that we still lack an understanding of relationships between form and function in certain taxonomic groups.

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Metabolic aspects of the secretion of stored compounds from blood platelets. The effect of NaF at different pH on nucleotide metabolism and function of washed platelets

Biochemical Journal ◽

10.1042/bj1940187 ◽

1981 ◽

Vol 194 (1) ◽

pp. 187-192 ◽

Cited By ~ 10

Author(s):

E H Mürer ◽

K Davenport ◽

E Siojo ◽

H J Day

Keyword(s):

Time Course ◽

Adenine Nucleotides ◽

Blood Platelets ◽

Fluoride Concentration ◽

Indirect Evidence ◽

Inhibitory Effect ◽

Nucleotide Metabolism ◽

Wide Range ◽

And Function ◽

Special Circumstances

The purpose of this study was to investigate the response of human blood platelets to fluoride at different pH. The results were as follows. (1) Fluoride induced secretion faster and at a lower concentration when pH was lowered. (2) Platelets exposed to 2 mM-fluoride at 0 degrees C at pH 5.3 underwent secretion when first pH and then temperature was raised, although no secretion was seen at 2 mM-fluoride concentration in the absence of the preincubation at low pH. (3) The concentration of [14C]ATP in platelets decreased steeply in response to fluoride before induction of secretion. Addition of antimycin blocked or partly inhibited secretion. Fluoride thus exerts an inhibitory effect on platelet glycolysis before induction of secretion. (4) Fluoride accumulated in the platelet pellet by a time course that preceded secretion. The accumulation was faster and greater at pH 6 than at 7.4. These four points are taken as indirect evidence that fluoride has to penetrate to the interior of the platelet to induce secretion. The activation takes place over a wide range of acid pH in contrast with induction of platelet function via the outside of the plasma membrane. In addition evidence is presented that the salvage pathway may under special circumstances play an important role in the re-synthesis of platelet adenine nucleotides.

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Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

10.1101/736843 ◽

2019 ◽

Cited By ~ 2

Author(s):

Diana J. Rennison ◽

Seth M. Rudman ◽

Dolph Schluter

Keyword(s):

Microbial Communities ◽

Local Adaptation ◽

Biotic Interactions ◽

Ecological Speciation ◽

Microbiome Composition ◽

Interacting Species ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

And Function ◽

Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

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iProteinDB: an integrative database of Drosophila post-translational modifications

10.1101/386268 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yanhui Hu ◽

Richelle Sopko ◽

Verena Chung ◽

Romain A. Studer ◽

Sean D. Landry ◽

...

Keyword(s):

Protein Interactions ◽

Protein Function ◽

Large Scale ◽

Model Organisms ◽

General Strategy ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Functional Sites ◽

Evolutionarily Conserved ◽

And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

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