Demographic history and local adaptation of Myripnois dioica (Asteraceae) provide insight on plant evolution in northern China flora

AbstractShort-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged <2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

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Population structure, demographic history and local adaptation of the grass carp

BMC Genomics ◽

10.1186/s12864-019-5872-1 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 7

Author(s):

Yubang Shen ◽

Le Wang ◽

Jianjun Fu ◽

Xiaoyan Xu ◽

Gen Hua Yue ◽

...

Keyword(s):

Population Structure ◽

Local Adaptation ◽

Grass Carp ◽

Demographic History

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Impacts of future climate change on urban flood volumes in Hohhot in northern China: benefits of climate change mitigation and adaptations

Hydrology and Earth System Sciences ◽

10.5194/hess-22-305-2018 ◽

2018 ◽

Vol 22 (1) ◽

pp. 305-316 ◽

Cited By ~ 14

Author(s):

Qianqian Zhou ◽

Guoyong Leng ◽

Maoyi Huang

Keyword(s):

Climate Change ◽

Local Adaptation ◽

Climate Change Mitigation ◽

Northern China ◽

Future Climate ◽

Future Climate Change ◽

Urban Flood ◽

Drainage Systems ◽

Rcp 8.5 ◽

Change Mitigation

Abstract. As China becomes increasingly urbanised, flooding has become a regular occurrence in its major cities. Assessing the effects of future climate change on urban flood volumes is crucial to informing better management of such disasters given the severity of the devastating impacts of flooding (e.g. the 2016 flooding events across China). Although recent studies have investigated the impacts of future climate change on urban flooding, the effects of both climate change mitigation and adaptation have rarely been accounted for together in a consistent framework. In this study, we assess the benefits of mitigating climate change by reducing greenhouse gas (GHG) emissions and locally adapting to climate change by modifying drainage systems to reduce urban flooding under various climate change scenarios through a case study conducted in northern China. The urban drainage model – Storm Water Management Model – was used to simulate urban flood volumes using current and two adapted drainage systems (i.e. pipe enlargement and low-impact development, LID), driven by bias-corrected meteorological forcing from five general circulation models in the Coupled Model Intercomparison Project Phase 5 archive. Results indicate that urban flood volume is projected to increase by 52 % over 2020–2040 compared to the volume in 1971–2000 under the business-as-usual scenario (i.e. Representative Concentration Pathway (RCP) 8.5). The magnitudes of urban flood volumes are found to increase nonlinearly with changes in precipitation intensity. On average, the projected flood volume under RCP 2.6 is 13 % less than that under RCP 8.5, demonstrating the benefits of global-scale climate change mitigation efforts in reducing local urban flood volumes. Comparison of reduced flood volumes between climate change mitigation and local adaptation (by improving drainage systems) scenarios suggests that local adaptation is more effective than climate change mitigation in reducing future flood volumes. This has broad implications for the research community relative to drainage system design and modelling in a changing environment. This study highlights the importance of accounting for local adaptation when coping with future urban floods.

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Demographic history and genomics of local adaptation in blue tit populations

Evolutionary Applications ◽

10.1111/eva.13035 ◽

2020 ◽

Vol 13 (6) ◽

pp. 1145-1165 ◽

Cited By ~ 1

Author(s):

Charles Perrier ◽

Quentin Rougemont ◽

Anne Charmantier

Keyword(s):

Local Adaptation ◽

Demographic History ◽

Blue Tit

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Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

10.1101/2020.04.05.026443 ◽

2020 ◽

Author(s):

Hugo Cayuela ◽

Yann Dorant ◽

Claire Mérot ◽

Martin Laporte ◽

Eric Normandeau ◽

...

Keyword(s):

Genetic Structure ◽

Reproductive Isolation ◽

Local Adaptation ◽

Population Genetic Structure ◽

Copy Number ◽

Population Genetic ◽

Demographic History ◽

Copy Number Variants ◽

Protein Coding ◽

Protein Coding Genes

AbstractIncreasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be important drivers of population genetic structure, whose study is generally restricted to the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local thermal conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene amplification. We also identified 175 CNVs associated with the divergence of three parapatric glacial lineages, of which 24% were located within protein-coding genes, which might contribute to genetic incompatibilities and ultimately, reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, that was very different from that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of markers in population genomics studies.

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Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia

10.21203/rs.3.rs-959635/v1 ◽

2021 ◽

Author(s):

Stephen M. Richards ◽

Leiting Li ◽

James Breen ◽

Nelli Hovhannisyan ◽

Oscar Estrada ◽

...

Keyword(s):

Nuclear Dna ◽

Demographic History ◽

Northern China ◽

Haplotype Network ◽

Bootstrap Support ◽

Hybridization Capture ◽

Chloroplast Genomes ◽

Broomcorn Millet ◽

Strong Bootstrap Support ◽

The Rich

Abstract Broomcorn millet (Panicum miliaceum L.) was domesticated in northern China at least 7,000 years ago and was subsequentially adopted as a cereal in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, a region that has an important history in crop domestication. The rich botanical material found at Areni-1 includes grains identified by morphology as broomcorn millet that were 14C dated to the medieval era (873 ± 36 CE and 1118 ± 35 CE). To retrace the demographic history of these broomcorn millet samples, we used ancient DNA extraction and hybridization capture enrichment to sequence and assemble three chloroplast genomes from the Areni-1 grains and then compared these sequences to 50 modern chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity and little inference on broomcorn demography could be made. However, in a phylogeny the chloroplast genomes separated into two clades with strong bootstrap support, similar to what has been reported for nuclear DNA from broomcorn millet. In a haplotype network, the chloroplast genomes of two accessions of wild (undomesticated) broomcorn millet contained a relatively large number of variants, 11 SNPs. These SNPs were not present in the domesticated varieties, suggesting these wild accessions may not be directly related to the lineages that underwent domestication or that broomcorn millet may have undergone a domestication bottleneck resulting in lost diversity in the chloroplast genome. These results demonstrate that broomcorn millet from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

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Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in Arabidopsis lyrata

10.1101/374900 ◽

2018 ◽

Author(s):

Tuomas Hämälä ◽

Outi Savolainen

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Demographic History ◽

Rate Variation ◽

Arabidopsis Lyrata ◽

Trade Offs ◽

Northern Latitudes ◽

Local Selection ◽

Empirical Level ◽

Selected Traits

AbstractShort-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory, but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modelling indicates that populations within the gradients diverged less than 2000 years ago and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high divergence and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

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Local adaptation to abiotic and biotic stresses and phenotypic selection on flowering time in annual Brachypodium spp. along an aridity gradient

10.1101/783779 ◽

2019 ◽

Author(s):

Shira Penner ◽

Yuval Sapir

Keyword(s):

Interspecific Competition ◽

Flowering Time ◽

Local Adaptation ◽

Eastern Mediterranean ◽

Plant Evolution ◽

Interactive Effects ◽

List Type ◽

Aridity Gradient ◽

Common Gardens ◽

The Impact

SummaryPlants have diverse strategies to cope with stress, including early flowering to “escape” abiotic stress and late flowering to mitigate biotic stress. Plants are usually exposed to multiple stresses simultaneously, but little is known about the impact of multiple co-occurring stresses on plant evolution.We tested for adaptation to both aridity and interspecific competition of the model plant Brachypodium spp., collected along the aridity gradient in Israel. We recorded flowering time and estimated fitness in a controlled watering experiment, with treatments mimicking Mediterranean and arid precipitation, and in two common gardens located in the extremes of the gradient (i.e., desert and mesic Mediterranean). At the latter we also manipulated interspecific competition to examine the combined effect of competition and aridity.Plants from arid environments always flowered earlier, but we found no selection on flowering time in the watering experiment. In the common gardens, however, the direction of selection on flowering time differed between sites and competition treatments.We conclude that interactions between aridity and competition drive local adaptation of Brachypodium in the Eastern Mediterranean basin. Variation in flowering time is an important adaptive mechanism to aridity and multiple selection agents can have interactive effects on the evolution of this trait.

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Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

10.1101/019430 ◽

2015 ◽

Author(s):

Valeria Montano ◽

Xavier Didelot ◽

Matthieu Foll ◽

Bodo Linz ◽

Richard Reinhardt ◽

...

Keyword(s):

Helicobacter Pylori ◽

Population Structure ◽

Local Adaptation ◽

Demographic History ◽

Gastric Diseases ◽

Whole Genome Analysis ◽

Necrosis Factor Alpha ◽

Worldwide Population ◽

H Pylori ◽

Global And Local

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole-genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g. transcription elongation factor NusA and tumor Necrosis Factor Alpha-Inducing Protein Tipα) and hitherto unknown functional genes.

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Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex

10.1101/2021.01.26.428274 ◽

2021 ◽

Author(s):

D.M. Leigh ◽

H.E.L. Lischer ◽

F. Guillaume ◽

C. Grossen ◽

T. Günther

Keyword(s):

Local Adaptation ◽

Genetic Drift ◽

Demographic History ◽

True Positive Rate ◽

Detection Methods ◽

True Positive ◽

Alpine Ibex ◽

Snp Data ◽

Outlier Loci ◽

Frequency Changes

AbstractIdentifying local adaptation in bottlenecked species is essential for effective conservation management. Selection detection methods are often applied to bottlenecked species and have an important role in species management plans, assessments of the species’ adaptive capacity, and looking for responses to major threats like climate change. Yet, the allele frequency changes driven by selection and exploited in selection detection methods, are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods may offer within bottlenecked populations. In this study, we used simulations to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). We used the meticulously recorded demographic history of the Alpine ibex to generate a comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in putative outliers identified through selection scans on empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more selection detection methods were combined. However, the true positive rates were consistently low and became essentially negligible after this increased stringency. Despite the detection of many putative outlier loci in the empirical Alpine ibex RADseq data, none met the threshold needed to distinguish them from genetic drift-driven false positives. Unfortunately, the low true positive rate also creates a paradox, by preventing the exclusion of recent local adaptation within the Alpine ibex.

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