scholarly journals A Few Stickleback Suffice for the Transport of Alleles to New Lakes

2019 ◽  
Vol 10 (2) ◽  
pp. 505-514 ◽  
Author(s):  
Jared Galloway ◽  
William A. Cresko ◽  
Peter Ralph
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
De Novo ◽  
Empirical Studies ◽  
Low Frequency ◽  
Small Fish ◽  
Marine Population ◽  
Standing Variation ◽  
Population Genomic ◽  
Genomic Studies

Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels of gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.

scholarly journals A few stickleback suffice for the transport of alleles to new lakes

2019 ◽  
Author(s):  
Jared Galloway ◽  
William A. Cresko ◽  
Peter Ralph
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
De Novo ◽  
Empirical Studies ◽  
Low Frequency ◽  
Small Fish ◽  
Marine Population ◽  
Standing Variation ◽  
Population Genomic ◽  
Genomic Studies

AbstractThreespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations show similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.

scholarly journals Limited potential for adaptation to climate change in a broadly distributed marine crustacean

2011 ◽  
Vol 279 (1727) ◽  
pp. 349-356 ◽  
Author(s):  
Morgan W. Kelly ◽  
Eric Sanford ◽  
Richard K. Grosberg
Keyword(s):  
Climate Change ◽  
Local Adaptation ◽  
Thermal Tolerance ◽  
Extinction Risk ◽  
Empirical Studies ◽  
Natural Populations ◽  
Adaptation To Climate Change ◽  
Isolated Populations ◽  
Tigriopus Californicus ◽  
Standing Variation

The extent to which acclimation and genetic adaptation might buffer natural populations against climate change is largely unknown. Most models predicting biological responses to environmental change assume that species' climatic envelopes are homogeneous both in space and time. Although recent discussions have questioned this assumption, few empirical studies have characterized intraspecific patterns of genetic variation in traits directly related to environmental tolerance limits. We test the extent of such variation in the broadly distributed tidepool copepod Tigriopus californicus using laboratory rearing and selection experiments to quantify thermal tolerance and scope for adaptation in eight populations spanning more than 17° of latitude. Tigriopus californicus exhibit striking local adaptation to temperature, with less than 1 per cent of the total quantitative variance for thermal tolerance partitioned within populations. Moreover, heat-tolerant phenotypes observed in low-latitude populations cannot be achieved in high-latitude populations, either through acclimation or 10 generations of strong selection. Finally, in four populations there was no increase in thermal tolerance between generations 5 and 10 of selection, suggesting that standing variation had already been depleted. Thus, plasticity and adaptation appear to have limited capacity to buffer these isolated populations against further increases in temperature. Our results suggest that models assuming a uniform climatic envelope may greatly underestimate extinction risk in species with strong local adaptation.

scholarly journals De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

2021 ◽  
Author(s):  
Magdalena Bohutínská ◽  
Vinzenz Handrick ◽  
Levi Yant ◽  
Roswitha Schmickl ◽  
Filip Kolář ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
De Novo ◽  
Empirical Studies ◽  
De Novo Mutation ◽  
Rapid Adaptation ◽  
De Novo Mutations ◽  
Standing Variation ◽  
Arabidopsis Arenosa ◽  
Meiosis Genes

Abstract A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.

scholarly journals Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

2021 ◽  
Author(s):  
Felix Moerman ◽  
Emanuel A. Fronhofer ◽  
Florian Altermatt ◽  
Andreas Wagner
Keyword(s):  
Gene Flow ◽  
Sexual Reproduction ◽  
Range Expansion ◽  
De Novo ◽  
Tetrahymena Thermophila ◽  
Ph Gradient ◽  
Genetic Changes ◽  
Experimental Range ◽  
Standing Variation ◽  
Genomic Adaptation

AbstractPopulations that expand their range can undergo rapid evolutionary adaptation, which can be aided or hindered by sexual reproduction and gene flow. Little is known about the genomic causes and consequences of such adaptation. We studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophila in landscapes with a uniform environment or a pH-gradient, both in the presence and absence of gene flow and sexual reproduction. We used pooled genome sequencing to identify genes subject to selection caused by the expanding range and by the pH-gradient. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH gradient additionally affected genes involved in ion balance, and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. Sexual reproduction affected both de novo mutation and standing genetic variation, whereas gene flow and the presence of a pH-gradient affected only standing variation. Sexual reproduction may have aided genetic adaptation during range expansion, but only in the absence of gene flow, which may have swamped expanding populations with maladapted alleles.

scholarly journals Coherence of Microcystis species revealed through population genomics

2019 ◽  
Author(s):  
Olga M. Pérez-Carrascal ◽  
Yves Terrat ◽  
Alessandra Giani ◽  
Nathalie Fortin ◽  
Charles W. Greer ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Geographic Location ◽  
Biological Species ◽  
Genomic Diversity ◽  
Cyanobacterial Blooms ◽  
Colony Morphology ◽  
Population Genomic

AbstractMicrocystis is a genus of freshwater cyanobacteria which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. However, colony morphology is a plastic trait which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes (of which 19 were resequenced to check for mutation in culture) mainly from Canada and Brazil. We identified eight Microcystis clusters of genomic similarity, only four of which correspond to named morphospecies and monophyletic groups. Notably, M. aeruginosa is paraphyletic, distributed across four genomic clusters, suggesting it is not a coherent species. Most monophyletic groups are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clusters further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes – including some involved in microcystin and micropeptin biosynthesis – are recombined between monophyletic groups in the same geographic location, suggesting local adaptation. Together, our results show the importance of using genomic criteria for Microcystis species delimitation and suggest the existence of locally adapted lineages and genes.ImportanceThe genus Microcystis is responsible for harmful and often toxic cyanobacterial blooms across the world, yet it is unclear how and if the genus should be divided into ecologically and genomically distinct species. To resolve the controversy and uncertainty surrounding Microcystis species, we performed a population genomic analysis of Microcystis genome from public databases, along with new isolates from Canada and Brazil. We inferred that significant genetic substructure exists within Microcystis, with several species being maintained by barriers to gene flow. Thus, Microcystis appears to be among a growing number of bacteria that adhere to a Biological Species-like Concept (BSC). Barriers to gene flow are permeable, however, and we find evidence for relatively frequent cross-species horizontal gene transfer (HGT) of genes that may be involved in local adaptation. Distinct clades of Microcystis (putative species) tend to have distinct profiles of toxin biosynthesis genes, and yet toxin genes are also subject to cross-species HGT and local adaptation. Our results thus pave the way for more informed classification, monitoring and understanding of harmful Microcystis blooms.

scholarly journals Recent African gene flow responsible for excess of old rare genetic variation in Great Britain

2017 ◽  
Author(s):  
Alexander Platt ◽  
Jody Hey
Keyword(s):  
Gene Flow ◽  
Allele Frequency ◽  
Rare Variants ◽  
Demographic History ◽  
Age Distribution ◽  
Low Frequency ◽  
African Populations ◽  
Rare Genetic Variation ◽  
Genomic Studies ◽  
The Uk

Population genomic studies can reveal the allele frequencies at millions of SNPs, with the numbers of observed low frequency SNPs increasing as more genomes are sequenced. Rare alleles tend to be younger than common alleles and are especially useful for studying demographic history, selection and heritability1,2. However, allele frequency can be a poor proxy for allele age, as genetic drift and natural selection can lead to alleles that are both rare and old. In order to allow joint assessments of allele frequency and allele age, a new estimator of allele age was developed that can be applied to variants of the lowest observed frequencies (singletons). By examining the geographic and age distribution of very rare variants in a large genomic sample from the UK3, we identify new evidence of gene flow from Africa into the ancestors of the modern UK population. A substantial proportion of variants with observed frequencies as low as 1.4 × 10‒4 are orders of magnitude older than can be explained without African gene flow and are found at much higher frequencies within modern African populations. We estimate that African populations contributed approximately 1.2% of the UK gene pool and did so approximately 400 years ago. These findings are relevant both to our understanding of human history and to the nature of rare variation segregating within populations: a variant that is rare because it is a recent mutation in the direct ancestor of the population will have had a very different evolutionary history than an ancient one that has persisted at high frequencies in a diverged population and only recently arrived through migration.

scholarly journals Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed

2021 ◽  
Author(s):  
Julia M Kreiner ◽  
George Sandler ◽  
Aaron J Stern ◽  
Patrick J. Tranel ◽  
Detlef Weigel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Herbicide Resistance ◽  
De Novo ◽  
Parallel Evolution ◽  
Selective Advantage ◽  
Past Century ◽  
Resistance Mutations ◽  
Standing Variation ◽  
Agricultural Weed

Causal mutations and their frequency in nature are well-characterized for herbicide resistance. However, we still lack understanding of the extent of parallelism in the mutational origin of target-site resistance (TSR), the role of standing variation and gene flow in the spread of TSR variants, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of Amaranthus tuberculatus, which we show to have undergone a massive expansion over the past century, with a contemporary Ne estimate of 8x107. We found nine TSR variants, three of which were common—showing extreme parallelism in mutational origin and an important role of gene flow in their geographic spread. The number of repeated origins varied across TSR loci and generally showed stronger signals of selection on de novo mutations, but with considerable evidence for selection on standing variation. Allele ages at TSR loci varied from ~10-250 years old, greatly predating the advent of herbicides. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We found evidence of haplotype competition between two TSR mutations, their successes in part modulated by either adaptive introgression of, or epistasis with, genome-wide resistance alleles. Together, this work reveals a remarkable example of spatial parallel evolution—the ability of independent mutations to spread due to selection contingent on not only the time, place, and background on which they arise but the haplotypes they encounter.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
A. Rose Brannon ◽  
Gowtham Jayakumaran ◽  
Monica Diosdado ◽  
Juber Patel ◽  
Anna Razumova ◽  
...  
Keyword(s):  
Cancer Patients ◽  
De Novo ◽  
Low Frequency ◽  
High Sensitivity ◽  
Clinical Analysis ◽  
De Novo Mutation ◽  
Cell Free Dna ◽  
Free Dna ◽  
Somatic Alterations ◽  
Mutation Profiling

AbstractCirculating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

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