scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Jonathan R. Meerbeek ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Related Species ◽  
Reference Genome ◽  
Genetic Differences ◽  
Genomic Diversity ◽  
Closely Related Species ◽  
Esox Masquinongy ◽  
Inbreeding Rate ◽  
Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window-based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears to be higher, presumably due to isolation of subpopulations, than the inbreeding rate of the Iowa population.Conclusions This study was the first to document that brood stock Muskellunge from Iowa showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. Finally, these results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Related Species ◽  
Reference Genome ◽  
Genetic Differences ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Closely Related Species ◽  
Esox Masquinongy ◽  
Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species. Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed a clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses. Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The inbreeding rate appears is presumably due to isolation of subpopulations. Conclusions This study is the first of its kind in Muskellunge from Iowa in which captured brood stock showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected . Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. These results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Jonathan Meerbeek ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Related Species ◽  
Reference Genome ◽  
Genetic Differences ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Closely Related Species ◽  
Esox Masquinongy ◽  
Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.ResultsVariant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed a clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears is presumably due to isolation of subpopulations.ConclusionsThis study is the first of its kind in Muskellunge from Iowa in which captured brood stock showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population.These results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

scholarly journals Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

2021 ◽  
Author(s):  
Josue Chinchilla-Vargas ◽  
Jonathan R. Meerbeek ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Management Practices ◽  
Genetic Difference ◽  
Variant Calling ◽  
Genomic Diversity ◽  
High Rate ◽  
Esox Masquinongy ◽  
High Quality Snps ◽  
Signatures Of Selection

Abstract Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with Fst values larger than 0.9. Canadian inbreeding rate (Froh=0.32) appears to be higher to the inbreeding of Iowa population (Froh=0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canada population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

scholarly journals Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1021
Author(s):  
Josue Chinchilla-Vargas ◽  
Jonathan R. Meerbeek ◽  
Max F. Rothschild ◽  
Francesca Bertolini
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Management Practices ◽  
Genetic Difference ◽  
Variant Calling ◽  
Principal Component ◽  
Genomic Diversity ◽  
High Rate ◽  
Esox Masquinongy ◽  
Signatures Of Selection

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

The Natural Groups of Species in the Genus Ips De Geer (Coleoptera: Scolytidae) in North America

1963 ◽  
Vol 95 (5) ◽  
pp. 508-516 ◽  
Author(s):  
G. R. Hopping
Keyword(s):  
North America ◽  
North American ◽  
Related Species ◽  
North American Species ◽  
Closely Related Species ◽  
The North ◽  
The World ◽  
Group Relationships ◽  
Natural Groups

AbstractThe genus Ips is one of four closely related genera in the tribe Ipini, sub-tribe Ipina (De Geer 1775, Balachowsky 1949, Nunberg 1954, Hopping 1963). There are now 32 species of Ips recognized in North America, with a few more as yet undescribed. This paper defines the groups of closely related species with observations on the group relationships of species from other parts of the world. Work is in progress to define the North American species in each group.

Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

2019 ◽  
Vol 24 (5) ◽  
pp. 866
Author(s):  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska ◽  
Anna Maria Bobowicz ◽  
Alina Bączkiewicz ◽  
Zbigniew Adamski ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Habitat Preferences ◽  
Abundant Species ◽  
Systematic Position ◽  
Genetic Differences ◽  
Similar Species ◽  
Closely Related Species ◽  
Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

A giant Permian fusulinid from east-central Alaska with comparisons of all giant fusulinids in western North America

1995 ◽  
Vol 69 (5) ◽  
pp. 805-812 ◽  
Author(s):  
Calvin H. Stevens
Keyword(s):  
North America ◽  
Related Species ◽  
The Other ◽  
Lower Permian ◽  
Early Permian ◽  
Western North America ◽  
Closely Related Species ◽  
East Central ◽  
West Texas ◽  
Species Groups

The discovery of a new locality yielding giant Guadalupian (Lower Permian) fusulinids in east-central Alaska extends the range of these forms much farther north than previously known, and into a tectonostratigraphic terrane from which they previously had not been reported. The number of areas from which giant parafusulinids are known in North America is thus raised to eight. Three of these localities are in rocks that previously had been referred to the allochthonous McCloud belt arc, and one, West Texas, is known to have been part of Paleozoic North America. Comparison of species from all areas suggests that there are two closely related species groups: one represented in Texas and Coahuila, and the other represented in Sonora, northern California, northeastern Washington, southern and northern British Columbia, Alaska, and apparently in Texas. These groups may differ because they are of slightly different ages or because interchange between the faunas of Texas–Coahuila area and the other regions was somewhat inhibited during the Early Permian.

Relocation of Alona manueli Sinev & Zawisza 2013 and a new closely related species from the Ecuadorian Andes to the new genus Alpinalona (Cladocera, Chydoridae, Aloninae)

Zootaxa ◽  
2017 ◽  
Vol 4350 (3) ◽  
pp. 563 ◽  
Author(s):  
MIGUEL ALONSO ◽  
ARTEM Y. SINEV
Keyword(s):  
North America ◽  
South America ◽  
High Altitude ◽  
Related Species ◽  
National Park ◽  
New Genus ◽  
Ventral Surface ◽  
Closely Related Species ◽  
Head Pores ◽  
Lateral Head

Alpinalona gen. nov. is described for two species found in high altitude localities of continental North America and South America: Alona manueli (Sinev & Zawisza, 2013) from the Neovolcanic Mexican Axis and Alpinalona cajasi gen. et sp. nov from El Cajas National Park (Ecuador). The new genus is separated from Hexalona and allies by the absence of limb VI and filter plate V;  from Anthalona, Coronatella and the elegans-group by having seven setae on exopodite III, and by the presence of a well-developed seta 1 on the IDL of limb III; from Alona s. str. (quadrangularis-group) and Ovalona, by two main head pores, lateral head pores located close to main pores, and by a bilobed exopodite V; from Ovalona by the presence of seta (i) and inner setae 2–3 on limb I, and setae 4–5 of exopodite III being of same size; and from Alona s. lato by weakly developed marginal denticles of postabdomen, clusters of thin setulae on ventral surface of limb I, and by plumose setae 5–6 of exopodite IV. Alpinalona cajasi sp. nov. can be easily distinguished from A. manueli by the following characteristics: prominent posterodorsal angle of carapace; broader headshield; longer PP distance; and postanal marginal denticles organized into groups.  

SEX ATTRACTANT BLENDS FOR STRAWBERRY CUTWORM, AMPHIPOEA INTEROCEANICA (SMITH), AND A CLOSELY RELATED SPECIES, AMPHIPOEA AMERICANA (SPEYER) (LEPIDOPTERA: NOCTUIDAE)

1987 ◽  
Vol 119 (3) ◽  
pp. 301-303
Author(s):  
D.L. Struble ◽  
G.L. Ayre ◽  
J.R. Byers
Keyword(s):  
North America ◽  
Convenient Method ◽  
Related Species ◽  
Sex Pheromones ◽  
Sex Attractant ◽  
Similar Species ◽  
Closely Related Species ◽  
Tetradecenyl Acetate ◽  
Important Pest ◽  
Lepidoptera Noctuidae

The strawberry cutworm, Amphipoea interoceanica (Smith), has recently become an important pest of strawberry plants in Manitoba (Ayre 1980) and Quebec (Mailloux and Bostanian 1985). Larvae damage or kill the plants and commercial plantings are sometimes heavily damaged. Strawberry cutworm is widely distributed in North America and is broadly sympatric with a morphologically similar species, Amphipoea americana (Speyer) (Forbes 1954), which is occasionally a pest of corn (Gibson 1920). Sex pheromones of these species have not been reported, although Roelofs and Comeau (1971) found that males of strawberry cutworm were attracted to (Z)-9-tetradecenyl acetate (abbrev. Z9- 14:Ac). A sex attractant for strawberry cutworm would provide a convenient method for monitoring population levels in the vicinity of strawberry fields.

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