Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

Abstract Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

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The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci

Journal of Heredity ◽

10.1093/jhered/esz007 ◽

2019 ◽

Vol 110 (4) ◽

pp. 494-513 ◽

Cited By ~ 1

Author(s):

Adam G Jones ◽

Stevan J Arnold ◽

Reinhard Bürger

Keyword(s):

Local Adaptation ◽

Evolutionary Biology ◽

Quantitative Traits ◽

Trait Divergence ◽

Genome Wide ◽

Outlier Loci ◽

Wide Range ◽

Marker Loci ◽

Neutral Marker ◽

Fst Outlier

Abstract With the advent of next-generation sequencing approaches, the search for individual loci underlying local adaptation has become a major enterprise in evolutionary biology. One promising method to identify such loci is to examine genome-wide patterns of differentiation, using an FST-outlier approach. The effects of pleiotropy and epistasis on this approach are not yet known. Here, we model 2 populations of a sexually reproducing, diploid organism with 2 quantitative traits, one of which is involved in local adaptation. We consider genetic architectures with and without pleiotropy and epistasis. We also model neutral marker loci on an explicit genetic map as the 2 populations diverge and apply FST outlier approaches to determine the extent to which quantitative trait loci (QTL) are detectable. Our results show, under a wide range of conditions, that only a small number of QTL are typically responsible for most of the trait divergence between populations, even when inheritance is highly polygenic. We find that the loci making the largest contributions to trait divergence tend to be detectable outliers. These loci also make the largest contributions to within-population genetic variance. The addition of pleiotropy reduces the extent to which quantitative traits can evolve independently but does not reduce the efficacy of outlier scans. The addition of epistasis, however, reduces the mean FST values for causative QTL, making these loci more difficult, but not impossible, to detect in outlier scans.

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Genomics of sorghum local adaptation to a parasitic plant

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1908707117 ◽

2020 ◽

Vol 117 (8) ◽

pp. 4243-4251 ◽

Cited By ~ 3

Author(s):

Emily S. Bellis ◽

Elizabeth A. Kelly ◽

Claire M. Lorts ◽

Huirong Gao ◽

Victoria L. DeLeo ◽

...

Keyword(s):

Genetic Diversity ◽

Local Adaptation ◽

Species Interactions ◽

Balancing Selection ◽

Control Plant ◽

Farming Systems ◽

Striga Hermonthica ◽

Loss Of Function ◽

Trade Offs ◽

Genome Wide

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

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Genomics of sorghum local adaptation to a parasitic plant

10.1101/633529 ◽

2019 ◽

Cited By ~ 1

Author(s):

Emily S. Bellis ◽

Elizabeth A. Kelly ◽

Claire M. Lorts ◽

Huirong Gao ◽

Victoria L. DeLeo ◽

...

Keyword(s):

Genetic Diversity ◽

Local Adaptation ◽

Striga Hermonthica ◽

Wild Plant ◽

Parasitic Weed ◽

Genome Wide ◽

Staple Crop ◽

Term Maintenance ◽

Maintenance Of Diversity

ABSTRACTHost-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential tradeoffs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and belowground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with tradeoffs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9 edited sorghum further indicate the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.SIGNIFICANCE STATEMENTUnderstanding co-evolution in crop-parasite systems is critical to management of myriad pests and pathogens confronting modern agriculture. In contrast to wild plant communities, parasites in agricultural ecosystems are usually expected to gain the upper hand in co-evolutionary ‘arms races’ due to limited genetic diversity of host crops in cultivation. Here, we develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. We find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for co-evolutionary dynamics in smallholder agroecosystems.

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Little plant, big city: a test of adaptation to urban environments in common ragweed ( Ambrosia artemisiifolia )

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.0968 ◽

2018 ◽

Vol 285 (1881) ◽

pp. 20180968 ◽

Cited By ~ 18

Author(s):

Amanda J. Gorton ◽

David A. Moeller ◽

Peter Tiffin

Keyword(s):

Flowering Time ◽

Local Adaptation ◽

Urban Environments ◽

Ambrosia Artemisiifolia ◽

Rural Populations ◽

Adaptive Divergence ◽

Transplant Experiment ◽

Native Plant ◽

Urban Populations ◽

Common Ragweed

A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, ( Ambrosia artemisiifolia ), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural field sites. This counter-gradient variation is consistent adaptive divergence between urban and rural populations. Also consistent with local adaptation, both urban and rural genotypes experienced stronger net selection in the foreign than in the local habitat, but this pattern was not significant for male fitness. Despite the evidence for local adaptation, rural populations had higher lifetime fitness at all sites, suggesting that selection has been stronger or more uniform in rural than urban populations. We also found that inter-population differences in both flowering time and fitness tended to be greater among urban than rural populations, which is consistent with greater drift or spatial variation in selection within urban environments. In summary, our results are consistent with adaptive divergence of urban and rural populations, but also suggest there may be greater environmental heterogeneity in urban environments which also affects evolution in urban landscapes.

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Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

BMC Evolutionary Biology ◽

10.1186/s12862-019-1559-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Zhigang Wu ◽

Xinwei Xu ◽

Juan Zhang ◽

Gerhard Wiegleb ◽

Hongwei Hou

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Environmental Factors ◽

Local Adaptation ◽

Aquatic Macrophyte ◽

Spatial Genetic Structure ◽

Long Distance ◽

Elevation Gradients ◽

Mantel Tests ◽

Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

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Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01137-0 ◽

2021 ◽

Author(s):

Diansi Yu ◽

Hui Wang ◽

Wei Gu ◽

Tao Qin ◽

Pingdong Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genotyping By Sequencing ◽

Germplasm Resources ◽

Genome Wide

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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