Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in
            Cornus florida
            L.—Insights from GWAS and GBS data

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as a repository and analytic framework for genomic, phenotypic, and environmental data for forest trees. One of key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals.

Download Full-text

Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

Download Full-text

CartograTree: Enabling landscape genomics for forest trees

10.7287/peerj.preprints.2345v2 ◽

2016 ◽

Author(s):

Nic Herndon ◽

Emily S Grau ◽

Iman Batra ◽

Steven A Demurjian Jr. ◽

Hans A Vasquez-Gross ◽

...

Keyword(s):

Population Structure ◽

Economic Value ◽

Genomic Data ◽

Environmental Data ◽

Geospatial Data ◽

Data Sets ◽

Forest Trees ◽

Analytic Framework ◽

Landscape Genomics ◽

The World

Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as a repository and analytic framework for genomic, phenotypic, and environmental data for forest trees. One of key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals.

Download Full-text

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

Science Advances ◽

10.1126/sciadv.abc6318 ◽

2020 ◽

Vol 6 (48) ◽

pp. eabc6318

Author(s):

Ira Cooke ◽

Hua Ying ◽

Sylvain Forêt ◽

Pim Bongaerts ◽

Jan M. Strugnell ◽

...

Keyword(s):

Climate Change ◽

Population Structure ◽

Skeletal Development ◽

Host Population ◽

Genomic Signatures ◽

Long Reads ◽

Adaptive Processes ◽

Acropora Tenuis ◽

Whole Genome Resequencing ◽

Genetic Signatures

Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species’ responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.

Download Full-text

The genomic basis of domestic colonisation and dispersal in Chagas disease vectors

10.1101/2021.04.27.441467 ◽

2021 ◽

Author(s):

Luis E Hernandez-Castro ◽

Anita G Villacís ◽

Arne Jacobs ◽

Bachar Cheaib ◽

Casey C Day ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Local Adaptation ◽

Chagas Disease ◽

Regional Scale ◽

Landscape Genomics ◽

Human Habitat ◽

Rhodnius Ecuadoriensis ◽

Genomic Adaptation ◽

Domestic Setting

AbstractThe biology of vector adaptation to the human habitat remains poorly understood for many arthropod-borne diseases but underpins effective and sustainable disease control. We adopted a landscape genomics approach to investigate gene flow, signatures of local adaptation, and drivers of population structure among multiple linked wild and domestic population pairs in Rhodnius ecuadoriensis, an important vector of Chagas Disease. Evidence of high triatomine gene flow (FST) between wild and domestic ecotopes at sites throughout the study area indicate insecticide-based control will be hindered by constant re-infestation of houses. Genome scans revealed genetic loci with strong signal of local adaptation to the domestic setting, which we mapped to annotated regions in the Rhodnius prolixus genome. Our landscape genomic mixed effects models showed Rhodnius ecuadoriensis population structure and connectivity is driven by landscape elevation at a regional scale. Our ecologically- and spatially-explicit vector dispersal model enables targeted vector control and recommends spatially discrete, periodic interventions to local authorities as more efficacious than current, haphazard approaches. In tandem, evidence for parallel genomic adaptation to colonisation of the domestic environment at multiple sites sheds new light on the evolutionary basis of adaptation to the human host in arthropod vectors.

Download Full-text