Editorial: The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context

Cushman, Samuel A.; Shirk, Andrew J.; Howe, Glenn T.; Murphy, Melanie A.; Dyer, Rodney J.; Joost, Stéphane

doi:10.3389/fgene.2018.00215

Cited by 12 publications

(13 citation statements)

References 3 publications

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“…The obtained genome information for F. suspensa will therefore be an essential resource for biological research and breeding. Here, we used genomic information in combination with a landscape genomics approach 2 to explore the genetic basis of the local adaptation of F. suspensa .…”

Section: Discussionmentioning

confidence: 99%

“…Spatial heterogeneity of the environment exerts differential selection pressures on natural populations, potentially leading to the local adaptation of a species across its range 1,2 . For naturally distributed plant species, selection pressure is mainly generated by abiotic factors such as soil chemistry, temperature, precipitation, and solar radiation 3 .…”

Section: Introductionmentioning

confidence: 99%

“…When molecular markers are used for analyses at the genome level, the role of natural selection in determining population genetic structure will be more readily measurable. Overall, the use of population genomics is helpful for understanding the genetic mechanisms of local species adaptation 2 .…”

Section: Introductionmentioning

confidence: 99%

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Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

Cushman

Yan

et al. 2020

Hortic Res

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Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

Cushman

Yan

et al. 2020

Hortic Res

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“…The continental margin of the Caribbean has been exposed to a wide variety of orogenic processes (Reyes et al, 2004) that have invoked changes in water bodies, consequently influencing the associated fauna. Based on a range of information on organism dynamics, the use of whole-genome sequence (WGS) data offers a high molecular resolution but is costly (Cushman et al, 2018). In order to generate an approximation of evolutionary histories and genetic inferences, we selected to use mitochondrial and nuclear genetic markers that offered a base line and good resolution of haplotype histories in A. latifrons.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of the Cichlid Andinoacara latifrons (Steindachner, 1878) as a Conservation Strategy in Different Colombian Basins

2020

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Cichlids constitute a diverse monophyletic group that have developed adaptive strategies to thrive in diverse environments. Andinoacara represents an example of diversification on the South American Andean uplift, providing a key model for understanding the evolution of biogeographic patterns. In this study, we analyzed the species Andinoacara latifrons using two mitochondrial markers (COI, cytb) and one nuclear marker (RAG1) in a populational level. Sequences were obtained through tissue collection and from the GenBank database. Populational analysis showed significant structuration among populations, also corroborated with population pairwise F st results. Fu's Fs and Tajima's D results showed populations that seems to be under populational expansion. We identified 22 haplotypes using cytb. The population associations in the Cauca haplotype are related to the Momposina depression and the mixture of the Cauca-Magdalena river basins in the lower Cauca-Magdalena region. We constructed a new phylogenetic tree, which grouped mainly two A. latifrons lineages: (1) an upper Magdalena and Catatumbo clade and (2) an upper Cauca and upper Magdalena clade. Thus, A. latifrons represents a diverse entity that contributes to our understanding of the evolutionary history of northern South America. Our findings provide insight into devising public policies in determining refuges for the preservation of biodiversity in the lower Cauca and Magdalena regions in Colombia.

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“…Microsatellite loci assumed or identified as being neutral are the most frequent type of markers used in landscape genetics (Storfer et al., 2010). Besides, SNP markers are now becoming widespread and can also be used to perform these analyses provided that loci under selective pressures (identified as outliers) have been discarded (Cushman et al., 2018; Foll & Gaggiotti, 2008). Accordingly, graph4lg functions use genetic data with two‐ or three‐digit allele coding to fit the common microsatellite coding.…”

Section: Workflowmentioning

confidence: 99%

graph4lg: A package for constructing and analysing graphs for landscape genetics in R

Savary

Foltête

Moal³

et al. 2020

Methods Ecol Evol

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Editorial: The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context

Cited by 12 publications

References 3 publications

Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

Genetic Diversity of the Cichlid Andinoacara latifrons (Steindachner, 1878) as a Conservation Strategy in Different Colombian Basins

graph4lg: A package for constructing and analysing graphs for landscape genetics in R

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