Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut ( Pterocarya stenoptera )

2020 ◽  
Author(s):  
Lin‐Feng Li ◽  
Samuel A. Cushman ◽  
Yan‐Xia He ◽  
Xiao‐Fei Ma ◽  
Xue‐Jun Ge ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genetic Evidence ◽  
Landscape Genomics ◽  
Pterocarya Stenoptera ◽  
Chinese Wingnut

scholarly journals Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau

2021 ◽  
Vol 118 (17) ◽  
pp. e2017831118
Author(s):  
Qingyun Liu ◽  
Haican Liu ◽  
Li Shi ◽  
Mingyu Gan ◽  
Xiuqin Zhao ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genetic Evidence ◽  
The Tibetan Plateau ◽  
Lower Altitude ◽  
Local Environments ◽  
Plausible Model ◽  
Genes Encoding

During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host–pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.

Genetic evidence of local adaptation of wheat yellow rust (Puccinia striiformis f. sp. tritici) within France

2005 ◽  
Vol 14 (7) ◽  
pp. 2065-2073 ◽  
Author(s):  
J. ENJALBERT ◽  
X. DUAN ◽  
M. LECONTE ◽  
M. S. HOVMØLLER ◽  
C. DE VALLAVIEILLE-POPE
Keyword(s):  
Local Adaptation ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Genetic Evidence

scholarly journals Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

2019 ◽  
Author(s):  
Alexandra K. Fraik ◽  
Mark J. Margres ◽  
Brendan Epstein ◽  
Soraia Barbosa ◽  
Menna Jones ◽  
...  
Keyword(s):  
Spatial Variation ◽  
Local Adaptation ◽  
Environmental Variables ◽  
Abiotic Factors ◽  
Rapid Onset ◽  
Tasmanian Devil ◽  
Landscape Genomics ◽  
Abiotic Environment ◽  
Candidate Loci ◽  
Sarcophilus Harrisii

AbstractLandscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment and/or by DFTD. We employ genetic-environment association (GEAs) analyses using a RAD-capture panel consisting of 6,886 SNPs from 3,286 individuals sampled pre- and post-disease arrival. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 349 unique loci linked to 64 genes, suggesting local adaptation to abiotic environment. Following DFTD arrival, however, we detected few of the pre-disease candidate loci, but instead frequencies of candidate loci linked to 14 genes correlated with disease prevalence. Loss of apparent signal of abiotic local adaptation following disease arrival suggests swamping by the strong selection imposed by DFTD. Further support for this result comes from the fact that post-disease candidate loci are in linkage disequilibrium with genes putatively involved in immune response, tumor suppression and apoptosis. This suggests the strength GEA associations of loci with the abiotic environment are swamped resulting from the rapid onset of a biotic selective pressure.

scholarly journals Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

2019 ◽  
Author(s):  
Jaakko S. Tyrmi ◽  
Jaana Vuosku ◽  
Juan J. Acosta ◽  
Zhen Li ◽  
Lieven Sterck ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
Local Adaptation ◽  
Large Scale ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Keystone Species ◽  
Evolutionary Genetics ◽  
Genomic Diversity ◽  
Landscape Genomics ◽  
Polygenic Adaptation

AbstractUnderstanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic background often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we found that several coding loci contribute to local adaptation. We also discovered a very large (ca. 300 Mbp) putative inversion with a signal of local adaptation, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out to the need for more attention towards multi-locus analysis of polygenic adaptation.

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