Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation inDrosophila melanogaster

Alan O. Bergland; Ray Tobler; Josefa González; Paul Schmidt; Dmitri Petrov

doi:10.1111/mec.13455

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

10.1101/009084 ◽

2014 ◽

Cited By ~ 2

Author(s):

Alan O. Bergland ◽

Ray Tobler ◽

Josefa Gonzalez ◽

Paul Schmidt ◽

Dmitri Petrov

Keyword(s):

Drosophila Melanogaster ◽

North America ◽

Local Adaptation ◽

Latitudinal Gradients ◽

Secondary Contact ◽

Clinal Variation ◽

Evolutionary Forces ◽

Genome Wide ◽

Spatially Varying ◽

Spatially Varying Selection

Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations ofDrosophila melanogastersampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation inD. melanogasterand provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.

Genotypic Variation in C and N Isotope Discrimination Suggests Local Adaptation of Heart-Leaved Willow

Tree Physiology ◽

10.1093/treephys/tpab010 ◽

2021 ◽

Author(s):

Yi Hu ◽

Robert D Guy ◽

Raju Y Soolanayakanahally

Keyword(s):

Isotopic Composition ◽

Local Adaptation ◽

N Uptake ◽

Genotypic Variation ◽

Carbon Isotopic Composition ◽

Genotypic Differences ◽

Clinal Variation ◽

Trade Off ◽

Uptake Efficiency ◽

N Uptake Efficiency

Abstract Plants acquire multiple resources from the environment and may need to adjust and/or balance their respective resource-use efficiencies to maximize grow and survival, in a locally adaptive manner. In this study, tissue and whole-plant carbon isotopic composition (δ13C) and C/N ratios provided long-term measures of use efficiencies for water (WUE) and nitrogen (NUE), and a nitrogen isotopic composition (δ15N) based mass balance model was used to estimate traits related to N uptake and assimilation in heart-leaved willow (Salix eriocephala Michx.). In an initial common garden experiment consisting of 34 populations, we found population level variation in δ13C, C/N and δ15N, indicating different patterns in WUE, NUE and N uptake and assimilation. Although there was no relationship between foliar δ13C and C/N ratios among populations, there was a significant negative correlation between these measures across all individuals, implying a genetic and/or plastic trade-off between WUE and NUE not associated with local adaptation. To eliminate any environmental effect, we grew a subset of 21 genotypes hydroponically with nitrate as the sole N-source, and detected significant variation in δ13C, δ15N and C/N ratios. Variation in δ15N was mainly due to genotypic differences in the nitrate efflux/influx ratio (E/I) at the root. Both experiments suggested clinal variation in δ15N (and thus N uptake efficiency) with latitude of origin, which may relate to water availability and could contribute to global patterns in ecosystem δ15N. There was a tendency for genotypes with higher WUE to come from more water replete sites with shorter and cooler growing seasons. We found that δ13C, C/N, and E/I were not inter-correlated, suggesting that selection of growth, WUE, NUE and N uptake efficiency can occur without trade-off.

The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome‐wide dynamics of local adaptation in a lizard

Ecology and Evolution ◽

10.1002/ece3.5872 ◽

2019 ◽

Vol 9 (24) ◽

pp. 14356-14367

Author(s):

Alejandro Llanos‐Garrido ◽

Javier Pérez‐Tris ◽

José A. Díaz

Keyword(s):

Local Adaptation ◽

Outlier Detection ◽

Genome Wide ◽

Combined Use

SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

10.1101/2022.01.12.476036 ◽

2022 ◽

Author(s):

Tiago da Silva Ribeiro ◽

José A Galván ◽

John E Pool

Keyword(s):

Genetic Differentiation ◽

Local Adaptation ◽

Genetic Variant ◽

Real Data ◽

Selective Sweeps ◽

Functional Categories ◽

Genome Scans ◽

Genome Wide ◽

A Genome ◽

Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

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.

Local adaptation, refugial isolation and secondary contact of Alpine populations of the land snail Arianta arbustorum

Journal of Molluscan Studies ◽

10.1093/mollus/eyt017 ◽

2013 ◽

Vol 79 (3) ◽

pp. 241-248 ◽

Cited By ~ 14

Author(s):

Martin Haase ◽

Susanne Esch ◽

Bernhard Misof

Keyword(s):

Local Adaptation ◽

Land Snail ◽

Secondary Contact ◽

Arianta Arbustorum

Spatial variation in susceptibility to infection in a snail–trematode interaction

Parasitology ◽

10.1017/s0031182099006538 ◽

2000 ◽

Vol 121 (4) ◽

pp. 395-401 ◽

Cited By ~ 24

Author(s):

A. C. KRIST ◽

C. M. LIVELY ◽

E. P. LEVRI ◽

J. JOKELA

Keyword(s):

Gene Flow ◽

Shallow Water ◽

Local Adaptation ◽

Deep Water ◽

Clinal Variation ◽

Sympatric Populations ◽

Host Condition ◽

Susceptibility To Infection ◽

Allopatric Populations ◽

Asymmetric Pattern

Parasites should be better at infecting hosts from sympatric populations than allopatric populations most of the time (parasite local adaptation). In a previous study of a population of snail parasites (Microphallus sp.) from Lake Alexandrina, New Zealand, we found that Microphallus was more infective to snails (Potamopyrgus antipodarum) in shallow water but not in deep water. Here, we repeated the original study and also monitored the development of the parasite. We found that parasites from shallow water were more infective to hosts from shallow water and developed more rapidly in these hosts. In contrast, parasites from deep water were not more infective to hosts from deep water and did not develop more rapidly in them. These results suggest clinal variation in the susceptibility of these snails, with shallow-water snails more susceptible than deep-water snails. We offer 2 possible explanations for these results. First, gene flow in the Microphallus population is primarily from shallow to deep water, leading to an asymmetric pattern of local adaptation. Alternatively, snails from shallow water may be more susceptible for reasons independent of gene flow, perhaps due to differences in host condition between habitats.

LOCAL ADAPTATION MAINTAINS CLINAL VARIATION IN MELANIN-BASED COLORATION OF EUROPEAN BARN OWLS (TYTO ALBA)

Evolution ◽

10.1111/j.1558-5646.2010.00969.x ◽

2010 ◽

Cited By ~ 10

Author(s):

Sylvain Antoniazza ◽

Reto Burri ◽

Luca Fumagalli ◽

Jérôme Goudet ◽

Alexandre Roulin

Keyword(s):

Local Adaptation ◽

Clinal Variation ◽

Tyto Alba ◽

Barn Owls

Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Genetics Selection Evolution ◽

10.1186/s12711-017-0360-z ◽

2017 ◽

Vol 49 (1) ◽

Cited By ~ 35

Author(s):

Salvatore Mastrangelo ◽

Marco Tolone ◽

Maria T. Sardina ◽

Gianluca Sottile ◽

Anna M. Sutera ◽

...

Keyword(s):

Candidate Genes ◽

Local Adaptation ◽

Potential Candidate ◽

Runs Of Homozygosity ◽

Genome Wide ◽

Genome Wide Scan

River network rearrangements promote speciation in lowland Amazonian birds

10.1101/2021.11.15.468717 ◽

2021 ◽

Author(s):

Lukas J Musher ◽

Melina Giakoumis ◽

James Albert ◽

Glaucia Del Rio ◽

Marco Rego ◽

...

Keyword(s):

Small Rivers ◽

River Networks ◽

Secondary Contact ◽

Small Populations ◽

Hybrid Speciation ◽

River Dynamics ◽

Species Complexes ◽

Genome Wide ◽

Potential Case ◽

Displacement Processes

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of river-barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry and secondary contact among populations. We sequenced genome-wide markers to evaluate histories of divergence and introgression in six Amazonian avian species-complexes. We first tested the assumption that rivers are barriers for these taxa and found that even relatively small rivers facilitate divergence. We then tested whether species diverged with gene flow and recovered reticulate histories for all species, including one potential case of hybrid speciation. Our results support the hypothesis that river dynamics promote speciation and reveal that many rainforest taxa are micro-endemic, unrecognized and thus threatened with imminent extinction. We propose that Amazonian hyper-diversity originates in part from fine-scale barrier displacement processes, including river dynamics, which allow small populations to differentiate and disperse into secondary contact.