scholarly journals Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

2016 ◽  
Vol 25 (18) ◽  
pp. 4488-4507 ◽  
Author(s):  
Darren E. Irwin ◽  
Miguel Alcaide ◽  
Kira E. Delmore ◽  
Jessica H. Irwin ◽  
Gregory L. Owens
Keyword(s):  
Recurrent Selection ◽  
Parallel Evolution ◽  
Genomic Regions ◽  
Ring Species

scholarly journals Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in greenish warblers

2016 ◽  
Author(s):  
Darren E. Irwin ◽  
Miguel Alcaide ◽  
Kira E. Delmore ◽  
Jessica H. Irwin ◽  
Gregory L. Owens
Keyword(s):  
Recurrent Selection ◽  
Parallel Evolution ◽  
Geographic Area ◽  
Genomic Variation ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Technological Developments ◽  
Greenish Warbler ◽  
Genomic Regions ◽  
Ring Species

AbstractRecent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13,013,950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically-conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models background selection, but are consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this “sweep-before-differentiation” model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.

scholarly journals Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

2014 ◽  
Vol 281 (1783) ◽  
pp. 20140012 ◽  
Author(s):  
Devon E. Pearse ◽  
Michael R. Miller ◽  
Alicia Abadía-Cardoso ◽  
John Carlos Garza
Keyword(s):  
Life History ◽  
Rainbow Trout ◽  
Parallel Evolution ◽  
Genomic Region ◽  
Life History Strategies ◽  
Strong Linkage Disequilibrium ◽  
Rapid Adaptation ◽  
Life History Variation ◽  
Standing Variation ◽  
Genomic Regions

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus)

2019 ◽  
Vol 110 (6) ◽  
pp. 684-695 ◽  
Author(s):  
Alan Garcia-Elfring ◽  
Rowan D H Barrett ◽  
Virginie Millien
Keyword(s):  
Climate Adaptation ◽  
Peromyscus Leucopus ◽  
Parallel Evolution ◽  
Thermal Adaptation ◽  
Synaptic Function ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Northern Margin ◽  
Genomic Signatures ◽  
Genomic Regions

Abstract Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.

scholarly journals Complex adaptive architecture of quantitative resistance erosion in a plant fungal pathogen

2021 ◽  
Author(s):  
Thomas Dumartinet ◽  
Sébastien Ravel ◽  
Véronique Roussel ◽  
Luis Pérez Vicente ◽  
Jaime Aguayo ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Quantitative Resistance ◽  
Parallel Evolution ◽  
Genetic Resistance ◽  
Biological Data ◽  
Caribbean Region ◽  
Adaptive Architecture ◽  
Complex Adaptive ◽  
Pathogen Populations ◽  
Genomic Regions

Plant pathogens often adapt to plant genetic resistance so characterization of the architecture under-lying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host se-lection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation be-tween haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly varia-ble across all the population pairs studied. These results suggest complex adaptive architecture un-derlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were highlighted in genomic regions combining annotation analysis with available biological data.

scholarly journals Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genus Trifolium (Fabaceae)

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130347 ◽  
Author(s):  
Kenneth M. Olsen ◽  
Nicholas J. Kooyers ◽  
Linda L. Small
Keyword(s):  
White Clover ◽  
Gene Loss ◽  
Parallel Evolution ◽  
Chemical Defence ◽  
Cyanogenic Glucosides ◽  
Additional Species ◽  
Gene Deletions ◽  
Biochemical Polymorphisms ◽  
Multiple Species ◽  
Genomic Regions

Variation in cyanogenesis (hydrogen cyanide release following tissue damage) was first noted in populations of white clover more than a century ago, and subsequent decades of research have established this system as a classic example of an adaptive chemical defence polymorphism. Here, we document polymorphisms for cyanogenic components in several relatives of white clover, and we determine the molecular basis of this trans-specific adaptive variation. One hundred and thirty-nine plants, representing 13 of the 14 species within Trifolium section Trifoliastrum , plus additional species across the genus, were assayed for cyanogenic components (cyanogenic glucosides and their hydrolysing enzyme, linamarase) and for the presence of underlying cyanogenesis genes ( CYP79D15 and Li , respectively). One or both cyanogenic components were detected in seven species, all within section Trifoliastrum ; polymorphisms for the presence/absence (PA) of components were detected in six species. In a pattern that parallels our previous findings for white clover, all observed biochemical polymorphisms correspond to gene PA polymorphisms at CYP79D15 and Li . Relationships of DNA sequence haplotypes at the cyanogenesis loci and flanking genomic regions suggest independent evolution of gene deletions within species. This study thus provides evidence for the parallel evolution of adaptive biochemical polymorphisms through recurrent gene deletions in multiple species.

scholarly journals Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.)

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1845
Author(s):  
Gabrielle Sousa Mafra ◽  
Janeo Eustáquio de Almeida Filho ◽  
Antônio Teixeira do Amaral Junior ◽  
Carlos Maldonado ◽  
Samuel Henrique Kamphorst ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Recurrent Selection ◽  
Breeding Population ◽  
Genomic Region ◽  
Growth And Yield ◽  
Trait Loci ◽  
Ear Height ◽  
Genomic Regions

The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.

scholarly journals Untangling structural factors and evolutionary drivers in nascent polyploids

2020 ◽  
Author(s):  
Julie Ferreira de Carvalho ◽  
Solenn Stoeckel ◽  
Frederic Eber ◽  
Maryse Lode-Taburel ◽  
Marie-Madeleine Gilet ◽  
...  
Keyword(s):  
Genome Stability ◽  
Recurrent Selection ◽  
Fourth Generation ◽  
Structural Factors ◽  
Meiotic Behavior ◽  
Combined Use ◽  
Polyploid Formation ◽  
Formation Type ◽  
Genomic Regions ◽  
Genome Stabilization

(1)Allopolyploids have globally higher fitness than their diploid progenitors however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. (2)Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid B. napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors and polyploid formation type. We evaluated the evolution of meiotic behavior, fertility and identified rearrangements in S1 to S9 lineages, to explore the positive consequences of euploid selection on B. napus genome stability. (3)Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a quasi disappearance of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number strongly depended on the genetic background and cytoplasm donor. (4)The combined use of both self-fertilisation and outcrossing as well as recurrent euploid selection, allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.

scholarly journals Parallel Genetic Origin of Foot Feathering in Birds

2020 ◽  
Vol 37 (9) ◽  
pp. 2465-2476
Author(s):  
Chiara Bortoluzzi ◽  
Hendrik-Jan Megens ◽  
Mirte Bosse ◽  
Martijn F L Derks ◽  
Bert Dibbits ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Parallel Evolution ◽  
Ectopic Expression ◽  
Genetic Origin ◽  
Animal Evolution ◽  
Transcription Regulator ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions ◽  
Feather Development

Abstract Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.

scholarly journals Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Kun Hu ◽  
Lei Zhang ◽  
Yong Yin ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Recurrent Selection ◽  
Epistatic Effect ◽  
Phenotypic Variance ◽  
Epistatic Qtl ◽  
Maize Domestication ◽  
Genomic Regions ◽  
Mapping Populations

Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

scholarly journals Historical and contemporary signatures of selection in response to transmissible cancer in the Tasmanian Devil (Sarcophilus harrisii)

2020 ◽  
Author(s):  
Amanda R. Stahlke ◽  
Brendan Epstein ◽  
Soraia Barbosa ◽  
Austin Patton ◽  
Sarah A. Hendricks ◽  
...  
Keyword(s):  
Recurrent Selection ◽  
Rapid Evolution ◽  
Tasmanian Devil ◽  
Management Actions ◽  
Devil Facial Tumour Disease ◽  
Evolutionary Response ◽  
Recent Emergence ◽  
Transmissible Cancer ◽  
Genomic Regions ◽  
Sarcophilus Harrisii

AbstractTasmanian devils (Sarcophilus harrisii) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independently evolved transmissible cancer suggest that transmissible cancers may be a recurrent feature in devils. We used a targeted sequencing approach, RAD-capture, to identify genomic regions subject to rapid evolution in approximately 2,500 devils as DFTD spread across the species range. We found evidence for genome-wide contemporary evolution, including 186 candidate genes related to cell cycling and immune response. We then searched for signatures of recurrent selection with a molecular evolution approach and found widespread evidence of historical positive selection in devils relative to other marsupials. We identified both contemporary and historical selection in 19 genes and enrichment for contemporary and historical selection independently in 22 gene sets. Nonetheless, the overlap between candidates for historical selection and for contemporary response to DFTD was lower than expected, supporting novelty in the evolutionary response of devils to DFTD. Our results can inform management actions to conserve adaptive capacity of devils by identifying high priority targets for genetic monitoring and maintenance of functional diversity in managed populations.

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