scholarly journals Divergent selection causes whole genome differentiation without physical linkage among the targets in Spodoptera frugiperda (Noctuidae)

2018 ◽  
Author(s):  
Kiwoong Nam ◽  
Sandra Nhim ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Nicolas Nègre ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Divergent Selection ◽  
Critical Conditions ◽  
Whole Genome ◽  
Genome Sequences ◽  
Evolutionary Forces ◽  
Genome Differentiation ◽  
Physical Linkage

ABSTRACTThe process of speciation involves whole genome differentiation by overcoming gene flow between diverging populations. We have ample knowledge which evolutionary forces may cause genomic differentiation, and several speciation models have been proposed to explain the transition from genetic to genomic differentiation. However, it is still unclear what are critical conditions enabling genomic differentiation in nature. The Fall armyworm, Spodoptera frugiperda, is observed as two sympatric strains that have different host-plant ranges, suggesting the possibility of ecological divergent selection. In our previous study, we observed that these two strains show genetic differentiation across the whole genome with an unprecedentedly low extent, suggesting the possibility that whole genome sequences started to be differentiated between the strains. In this study, we analyzed whole genome sequences from these two strains from Mississippi to identify critical evolutionary factors for genomic differentiation. The genomic Fst is low (0.017) while 91.3% of 10kb windows have Fst greater than 0, suggesting genome-wide differentiation with a low extent. We identified nearly 400 outliers of genetic differentiation between strains, and found that physical linkage among these outliers is not a primary cause of genomic differentiation. Fst is not significantly correlated with gene density, a proxy for the strength of selection, suggesting that a genomic reduction in migration rate dominates the extent of local genetic differentiation. Our analyses reveal that divergent selection alone is sufficient to generate genomic differentiation, and any following diversifying factors may increase the level of genetic differentiation between diverging strains in the process of speciation.

scholarly journals Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

2019 ◽  
Author(s):  
Kiwoong NAM ◽  
Sandra Nhim ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Nicolas Nègre ◽  
...  
Keyword(s):  
Positive Selection ◽  
Driving Force ◽  
Migration Rate ◽  
Early Stage ◽  
Fall Armyworm ◽  
Whole Genome ◽  
Low Level ◽  
Evolutionary Forces ◽  
Genome Differentiation ◽  
Genetic Linkages

Abstract Background: The process of speciation inherently involves the transition from genetic to genomic differentiation. In the absence of a geographic barrier, the whole genome differentiation may occur only when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that whole genome differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for the whole genome differentiation in the fall armyworm. Results: We found that these two strains exhibit a low level of genomic differentiation (Fst = 0.0176), while 91.3% of 10kb windows have genetically differentiated sequences (Fst > 0). We observed that a genomic reduction in migration rate due to combined effects of mild positive selection and genetic linkages to selectively targeted loci are responsible for the whole genome differentiation. Phylogenetic analysis shows that positive selection generates the whole genome differentiation by sub-setting of variants in one strain from the other. Conclusions: From these results, we concluded that positive selection alone is sufficient for whole genome differentiation during the process of speciation. This study demonstrates that the propensity of adaptation alone determines the speciation events, suggesting that adaptive evolution is a single critical driving force for species diversity.

scholarly journals Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

2020 ◽  
Author(s):  
Katrina A. Schlum ◽  
Kurt Lamour ◽  
Caroline Placidi de Bortoli ◽  
Rahul Banerjee ◽  
Scott J. Emrich ◽  
...  
Keyword(s):  
United States ◽  
Puerto Rico ◽  
Gene Flow ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
The United States ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Long Distance ◽  
Host Strains

AbstractThe fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of >80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and the United States (USA) were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest panmixia in this population, other than a minor reduction in gene flow between the two overwintering populations in the continental USA that also corresponded to genetically distinct host strains. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Comparisons between laboratory-reared and field collected S. frugiperda support similar genomic diversity, validating the experimental use of laboratory strains. Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations.

scholarly journals Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Katrina A. Schlum ◽  
Kurt Lamour ◽  
Caroline Placidi de Bortoli ◽  
Rahul Banerjee ◽  
Robert Meagher ◽  
...  
Keyword(s):  
United States ◽  
Puerto Rico ◽  
Gene Flow ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
The United States ◽  
Whole Genome ◽  
Long Distance ◽  
Field Samples ◽  
Host Strains

Abstract Background The fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of > 80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). The population genomics of the United States (USA) fall armyworm remains poorly characterized to date despite its agricultural threat. Results In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and USA were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest a panmictic S. frugiperda population, with only a minor reduction in gene flow between the two overwintering populations in the continental USA, also corresponding to distinct host strains at the mitochondrial level. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Conclusions Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations. Based on the genomic similarities found between host strains and laboratory vs. field samples, our findings validate the experimental use of laboratory strains and the host strain differentiation based on mitochondria and sex-linked genetic markers extends to minor genome wide differences with some exceptions showing mixture between host strains is likely occurring in field populations.

scholarly journals Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Kiwoong Nam ◽  
Sandra Nhim ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Nicolas Nègre ◽  
...  
Keyword(s):  
Positive Selection ◽  
Genetic Linkage ◽  
Early Stage ◽  
Synergistic Effects ◽  
Fall Armyworm ◽  
Whole Genome ◽  
Low Level ◽  
Evolutionary Forces ◽  
Speciation Process ◽  
Evolutionary Force

Abstract Background The process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host–plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm. Results These two strains exhibit a low level of genomic differentiation (FST = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (FST > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other. Conclusions From these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.

Neanderthals and modern humans

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Homo Sapiens ◽  
Whole Genome ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Homo Neanderthalensis ◽  
Modern Mind ◽  
Similarities And Differences ◽  
Mode 3

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.

scholarly journals Insecticide resistance monitoring for the invasive populations of fall armyworm, Spodoptera frugiperda in China

2021 ◽  
Vol 20 (3) ◽  
pp. 783-791 ◽  
Author(s):  
Dan-dan ZHANG ◽  
Yu-tao XIAO ◽  
Peng-jun XU ◽  
Xian-ming YANG ◽  
Qiu-lin WU ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Resistance Monitoring
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