Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants

AbstractExtant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.

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Loss of genetic diversity reduces ability to adapt

10.1093/oso/9780198783398.003.0004 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Change ◽

Adaptive Evolution ◽

Extinction Risk ◽

Genomic Diversity ◽

Effective Population ◽

Evolutionary Potential ◽

Medium Term ◽

Loss Of Genetic Diversity ◽

New Mutations

Environmental change is a ubiquitous feature of the conditions faced by species, so they must either evolve, move to avoid threats, or perish. Species require genetic diversity to evolve to cope with environmental change through natural selection (adaptive evolution). The ability of populations to undergo adaptive evolution depends upon the strength of selection, genetic diversity, effective population size, mutation rates and number of generations. Loss of genetic diversity in small populations reduces their ability to evolve to cope with environmental change, thus increasing their extinction risk. Adaptive evolution in the short to medium term predominantly utilizes pre-existing genetic diversity, but new mutations make increasing contributions in later generations. Evolutionary potential can be estimated from the heritability of fitness in the environment of interest, or by extrapolation from genomic diversity.

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Eco-evolutionary community turnover following environmental change

10.1101/285288 ◽

2018 ◽

Author(s):

Jesse R. Lasky

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Environmental Change ◽

Community Dynamics ◽

Environmental Gradients ◽

Interspecific Variation ◽

Community Response ◽

High Gene Flow ◽

High Gene ◽

Response To Environmental Change

AbstractCo-occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co-occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can promote genetic diversity of traits under selection within populations. Here I build off existing quantitative genetic theory to study community dynamics of locally adapted species in response to temporal environmental change. I show that species with greater gene flow have lower equilibrium population size due to maladaptive immigrant genotypes (migration load). However, following abrupt environmental change that leaves all species initially maladapted, high gene flow species adapt faster due to greater standing genetic diversity. As a result, communities may undergo a transient reversal in relative abundance, sometimes only after substantial lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. High gene flow species can sometimes increase abundance under environmental change if environmental change supresses superior competitor but lower gene flow species. The community dynamics observed here parallel the purely ecological successional dynamics following disturbances and are analogous to the transient benefit of hypermutator alleles under changing environments. My results demonstrate how interspecific variation in life history can have far-reaching impacts on eco-evolutionary community response to environmental change.

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Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1714950115 ◽

2018 ◽

Vol 115 (10) ◽

pp. E2284-E2291 ◽

Cited By ~ 30

Author(s):

Sean F. Ryan ◽

Jillian M. Deines ◽

J. Mark Scriber ◽

Michael E. Pfrender ◽

Stuart E. Jones ◽

...

Keyword(s):

Genetic Diversity ◽

Hybrid Zone ◽

Zone Model ◽

Hybrid Zones ◽

Papilio Glaucus ◽

Evolutionary Trajectory ◽

Developmental Threshold ◽

Papilio Canadensis ◽

Nonlinear Responses ◽

Conservation And Management

Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity, and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over the course of a 32-y period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68-km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40-km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization, and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55–144 km/1 °C), shape, and contiguity of movement. Our findings suggest that the presence of nonclimatic barriers (e.g., genetic incompatibilities) and/or nonlinear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the geography of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones, and thus have implications for the conservation and management of genetic diversity.

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Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species

Genetics ◽

10.1093/genetics/152.2.713 ◽

1999 ◽

Vol 152 (2) ◽

pp. 713-727 ◽

Cited By ~ 19

Author(s):

Loren H Rieseberg ◽

Jeannette Whitton ◽

Keith Gardner

Keyword(s):

Genetic Study ◽

Genetic Architecture ◽

Chromosomal Rearrangements ◽

Pollen Sterility ◽

Model Organisms ◽

Hybrid Zones ◽

Reproductive Barriers ◽

Natural Hybrid ◽

Generation Times ◽

Helianthus Petiolaris

Abstract Genetic analyses of reproductive barriers represent one of the few methods by which theories of speciation can be tested. However, genetic study is often restricted to model organisms that have short generation times and are easily propagated in the laboratory. Replicate hybrid zones with a diversity of recombinant genotypes of varying age offer increased resolution for genetic mapping experiments and expand the pool of organisms amenable to genetic study. Using 88 markers distributed across 17 chromosomes, we analyze the introgression of chromosomal segments of Helianthus petiolaris into H. annuus in three natural hybrid zones. Introgression was significantly reduced relative to neutral expectations for 26 chromosomal segments, suggesting that each segment contains one or more factors that contribute to isolation. Pollen sterility is significantly associated with 16 of these 26 segments, providing a straightforward explanation of why this subset of blocks is disadvantageous in hybrids. In addition, comparison of rates of introgression across colinear vs. rearranged chromosomes indicates that close to 50% of the barrier to introgression is due to chromosomal rearrangements. These results demonstrate the utility of hybrid zones for identifying factors contributing to isolation and verify the prediction of increased resolution relative to controlled crosses.

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Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity.

Genetics ◽

10.1093/genetics/119.4.981 ◽

1988 ◽

Vol 119 (4) ◽

pp. 981-990

Author(s):

S Jana ◽

L N Pietrzak

Keyword(s):

Genetic Diversity ◽

Eastern Mediterranean ◽

Hordeum Spontaneum ◽

Hordeum Vulgare L ◽

Closely Related Species ◽

Mediterranean Countries ◽

Isozyme Loci ◽

Cultivated Barley ◽

Multilocus Associations ◽

High Degree

Abstract Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species.

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Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

Plant Genetic Resources ◽

10.1017/s1479262114000525 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S125-S129

Author(s):

Gi-An Lee ◽

Sok-Young Lee ◽

Ho-Sun Lee ◽

Kyung-Ho Ma ◽

Jae-Gyun Gwag ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Management ◽

Underutilized Crops ◽

Crop Species ◽

Closely Related Species ◽

Polymorphic Loci ◽

Allele Number ◽

The Mean ◽

Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

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Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

10.21203/rs.3.rs-56651/v1 ◽

2020 ◽

Author(s):

Mansoor Kodori ◽

Zohreh Ghalavand ◽

Abbas Yadegar ◽

Gita Eslami ◽

Masoumeh Azimirad ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Disease Severity ◽

Genetic Variants ◽

Rflp Analysis ◽

Clostridioides Difficile ◽

Pcr Rflp ◽

The Common ◽

Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

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Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2

Acta Naturae ◽

10.32607/actanaturae.11337 ◽

2021 ◽

Vol 13 (3) ◽

pp. 77-89

Author(s):

Aleksandra A. Nikonova ◽

Eugene B. Faizuloev ◽

Anastasia V. Gracheva ◽

Igor Yu. Isakov ◽

Vitaly V. Zverev

Keyword(s):

Genetic Diversity ◽

Genetic Variants ◽

Large Scale ◽

Biological Properties ◽

Viral Genomes ◽

Biological Features ◽

Health Measures ◽

Common Genetic Variants ◽

Coronavirus Infection ◽

The Relationship

The new coronavirus infection (COVID-19) represents a challenge for global health. Since the outbreak began, the number of confirmed cases has exceeded 117 million, with more than 2.6 million deaths worldwide. With public health measures aimed at containing the spread of the disease, several countries have faced a crisis in the availability of intensive care units. Currently, a large-scale effort is underway to identify the nucleotide sequences of the SARS-CoV-2 coronavirus that is an etiological agent of COVID-19. Global sequencing of thousands of viral genomes has revealed many common genetic variants, which enables the monitoring of the evolution of SARS-CoV-2 and the tracking of its spread over time. Understanding the current evolution of SARS-CoV-2 is necessary not only for a retrospective analysis of the new coronavirus infection spread, but also for the development of approaches to the therapy and prophylaxis of COVID-19. In this review, we have focused on the general characteristics of SARS-CoV-2 and COVID-19. Also, we have analyzed available publications on the genetic diversity of the virus and the relationship between the diversity and the biological properties of SARS-CoV-2, such as virulence and contagiousness.

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Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

10.1101/2020.06.13.150334 ◽

2020 ◽

Author(s):

Katherine M. Eaton ◽

Moisés A. Bernal ◽

Nathan J.C. Backenstose ◽

Trevor J. Krabbenhoft

Keyword(s):

Local Adaptation ◽

Environmental Gradients ◽

Parallel Evolution ◽

Amplicon Sequencing ◽

Species Flock ◽

Closely Related Species ◽

Oxford Nanopore ◽

Opsin Genes ◽

Potential Case ◽

Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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Prevalence and Adaptive Impact of Introgression

Annual Review of Genetics ◽

10.1146/annurev-genet-021821-020805 ◽

2021 ◽

Vol 55 (1) ◽

Author(s):

Nathaniel B. Edelman ◽

James Mallet

Keyword(s):

Genetic Variation ◽

Adaptive Evolution ◽

Genetic Variants ◽

Genomic Data ◽

Annual Review ◽

Publication Date ◽

Adaptive Introgression ◽

Changing Environments ◽

Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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