Genomic variation associated with local adaptation of weedy rice during de-domestication

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

Download Full-text

Intraspecific genomic variation and local adaptation in a young hybrid species

Molecular Ecology ◽

10.1111/mec.15760 ◽

2020 ◽

Author(s):

Angélica Cuevas ◽

Mark Ravinet ◽

Glenn‐Peter Sætre ◽

Fabrice Eroukhmanoff

Keyword(s):

Local Adaptation ◽

Genomic Variation ◽

Hybrid Species

Download Full-text

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

10.1101/744797 ◽

2019 ◽

Author(s):

Matthew JS Gibson ◽

Leonie C Moyle

Keyword(s):

Local Adaptation ◽

Structural Equation ◽

Genomic Variation ◽

Equation Modeling ◽

Nucleotide Polymorphisms ◽

Evaporative Demand ◽

Abiotic Environment ◽

Wild Tomato Species ◽

Tomato Species ◽

Wide Range

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms) with climate and geography, among 140 wild accessions. RDA, SEM, and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP-environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.

Download Full-text

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

10.1101/568725 ◽

2019 ◽

Cited By ~ 1

Author(s):

Colin R. Mahony ◽

Ian R. MacLachlan ◽

Brandon M. Lind ◽

Jeremy B. Yoder ◽

Tongli Wang ◽

...

Keyword(s):

Spatial Scale ◽

Local Adaptation ◽

Lodgepole Pine ◽

Genomic Data ◽

Genomic Variation ◽

Similar Species ◽

Adaptive Variation ◽

Phenotypic Data ◽

Standing Variation ◽

Climatic Drivers

AbstractThe need for tools to cost-effectively identify adaptive variation within ecologically and economically important plant species is mounting as the detrimental effects of climate change become increasingly apparent. For crop and wild populations alike, mismatches between adaptive variation and climatic optima will reduce health, growth, survival, reproduction, and continued establishment. The ease with which land managers can quantify the relative importance of different climate factors or the spatial scale of local adaptation to climate will have direct implications for the potential of mitigating or resolving such risks. Using seed collected from 281 provenances of lodgepole pine (Pinus contorta) from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that genomic and climate data are nearly equivalent for describing local adaptation in seedling traits. We also find strong agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with cold injury occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than are indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.

Download Full-text

Phenotypic Differentiation between Weedy Rice Populations Associated with their Local Adaptation in Early-and Late-Season Rice Fields

10.21203/rs.3.rs-1123645/v1 ◽

2021 ◽

Author(s):

Zhi Wang ◽

Xiao-Qi Jiang ◽

Xing-xing Cai ◽

Qi-Yu Xia ◽

Bao-Rong Lu

Keyword(s):

Flowering Time ◽

Local Adaptation ◽

Reproductive Traits ◽

Common Garden ◽

Rice Fields ◽

Day Length ◽

Weedy Rice ◽

Early Season ◽

Late Season ◽

Late Rice

Abstract Background: Temperatures and photoperiods can profoundly affect plant growth and development and play vital roles in the local adaptation of plant species. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, and it was found in the same rice fields (sympatry) of early and late rice-cultivation seasons in Leizhou, Guangdong Province of China. Generally, the phenological conditions, such as temperature and photoperiod, are different in the two seasons. Therefore, the early- and late-season weedy rice populations in the same rice fields provide a perfect system for estimating sympatric divergence in plant species. The previous study had demonstrated considerable genetic divergence between the early- and late-season weedy rice populations. Here, we designed in situ common garden experiments to estimate the phenotypical differences between the two-season weedy rice populations and disclose the local adaptation in weedy rice populations associated with their ambient temperature and photoperiod.Results: Distinct air temperature and day length variation patterns were recognized between the early and late rice-cultivation seasons, based on the 10-year historical climate data. More stressful conditions, indicated by low air temperature and long day length, were found for weedy rice growth in the early seasons. Noticeably, significant differences in plant heights, the number of tillers, flowering time, and reproductive traits were detected between the two-season weedy rice populations according to the early-season common garden experiment. The early-season populations showed evident higher plant heights, more tillers, and earlier flowering time than the late-season populations. However, such differences were not detected in the late-season common garden experiment. In addition, evident local adaptation represented by the traits such as plant heights, flowering time, and reproductive traits was only detected in the early-season weedy rice populations. The principal component analysis also showed clear population clusters between the two-season populations using the phenotypical data.Conclusions: This study provided clear evidence of phenotypic differentiation between the sympatric early- and late-season weedy rice populations, probably associated with the local adaptation to their ambient temperature and photoperiod. Our findings also have potential roles in facilitating the design of strategies for effective weedy rice control practices.

Download Full-text

Local adaptation and sexual selection drive intra-island diversification in a songbird lineage: differential divergence in autosomes and sex chromosomes

10.1101/353771 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yann XC Bourgeois ◽

Joris AM Bertrand ◽

Boris Delahaie ◽

Hélène Holota ◽

Christophe Thébaud ◽

...

Keyword(s):

Sexual Selection ◽

Natural Selection ◽

Reproductive Isolation ◽

Local Adaptation ◽

Sex Chromosomes ◽

Genomic Variation ◽

Color Variation ◽

Mating Signals ◽

Genome Wide

AbstractRecently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to test the relative importance of two major evolutionary mechanisms, adaptation to local ecological conditions by natural selection, or mechanisms of reproductive isolation such as assortative mating mediated by sexually selected mating signals or post-zygotic incompatibilities. Whereas local adaptation is expected to affect many loci throughout the genome, traits acting as mating signals are expected to be located on sex chromosomes and have a simple genetic basis. We used genome-wide markers to test these predictions in Reunion Island’s gray-white eye (Zosterops borbonicus), which has recently diversified into five distinct plumage forms. Two of them correspond to a polymorphic highland population that is separated by a steep ecological gradient from three distinct lowland forms that show narrow contact zones in plumage color traits, yet no association with environmental variables. An analysis of population structure using genome-wide SNP loci revealed two major clades corresponding to highland and lowland forms, respectively, with the latter separated further into three independent lineages corresponding to plumage forms. Coalescent tests of alternative demographic scenarios provided support for divergence of highland and lowland lineages with an intensification of gene flow in the last 60,000 years. Landscapes of genomic variation revealed that signatures of selection associated with elevation are found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. A gene ontology analysis identified TYRP1, a Z-linked color gene, as a likely candidate locus underlying color variation among lowland forms. Our results are consistent with the role of natural selection in driving the divergence of locally adapted highland populations, and the role of sexual selection in differentiating lowland forms through reproductive isolation mechanisms, showing that both modes of lineage divergence can take place at very small geographic scales in birds.

Download Full-text

Genomic analyses provide insights into peach local adaptation and responses to climate change

10.1101/2020.01.15.907709 ◽

2020 ◽

Author(s):

Yong Li ◽

Ke Cao ◽

Nan Li ◽

Gengrui Zhu ◽

Weichao Fang ◽

...

Keyword(s):

Local Adaptation ◽

Cold Hardiness ◽

Association Studies ◽

Sugar Content ◽

Evolutionary Genetics ◽

Genomic Variation ◽

Genome Wide ◽

Environmental Association ◽

Molecular Bases ◽

Bloom Date

The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map by re-sequencing genomes of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach local adaptation to diverse climates comprehensively. A total of 2,092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using GWEAS, a total of 3,496 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UV-B, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 years of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds valuable genome resources and candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and future breeding.

Download Full-text

Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

10.1101/440552 ◽

2018 ◽

Author(s):

Maribet Gamboa ◽

Kozo Watanabe

Keyword(s):

Local Adaptation ◽

Latitudinal Gradient ◽

Sequence Similarity ◽

Genomic Variation ◽

Environmental Drivers ◽

Genome Comparison ◽

Candidate Snps ◽

Nucleotide Polymorphisms ◽

High Sequence Similarity ◽

Geographical Regions

AbstractBackgroundEnvironmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan.ResultsA total of 4,251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome–genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process.ConclusionsOur results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts.

Download Full-text

Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

10.22541/au.162854295.58977249/v1 ◽

2021 ◽

Author(s):

Aglaia Antoniou ◽

Tereza Manousaki ◽

Francisco Ramírez ◽

Alessia Cariani ◽

Rita Cannas ◽

...

Keyword(s):

Local Adaptation ◽

Dynamic Equilibrium ◽

Natural Populations ◽

Spatial Dimension ◽

Western Mediterranean ◽

Genomic Variation ◽

Entire Genome ◽

Outlier Loci ◽

Genomic Approach ◽

Nw Mediterranean

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.

Download Full-text