scholarly journals Save Our Species: A Blueprint for Restoring Butternut (Juglans cinerea) across Eastern North America

2020 ◽  
Author(s):  
Carolyn C Pike ◽  
Martin Williams ◽  
Andrea Brennan ◽  
Keith Woeste ◽  
James Jacobs ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Species Abundance ◽  
Resistance Breeding ◽  
Eastern North America ◽  
Suitable Habitat ◽  
Isolated Populations ◽  
Closely Related Species ◽  
Range Edge ◽  
Moderate Resistance

Abstract Butternut is a relatively uncommon hardwood tree native to eastern North America. The species’ abundance has declined over the past 50 years, primarily because of an invasive pathogen (Ophiognomonia clavigignenti-juglandacearum [Oc-j]) and loss of suitable habitat for regeneration. Although genetic diversity of butternut is highest along the southern range edge, genetic diversity rangewide is fairly high, except in small and isolated populations. Although there is little evidence for even moderate resistance in native butternut, hybrids with Japanese walnut, a closely related species, display enough tolerance to infection to persist on the landscape and bear abundant nut crops year after year. Cryostorage of native embryogenic axes has yielded promising initial results as a strategy for gene conservation, but additional action is needed to conserve the remaining native gene pool. We describe a strategy for canker-resistance breeding in butternut using naturally occurring hybrids, hybrids in research orchards, and sources of native trees from as many regions as possible. Forest managers are encouraged to find surviving trees and collect seed for planting in suitable habitat to develop actionable knowledge that will enable the restoration of butternut with enough resistance to be self-sustaining on the landscape.

Notes on the Life-history and Habits of the Brown Mite, Bryobia arborea Morgan & Anderson (Acarina: Tetranychidae), on Peach in Ontario

1960 ◽  
Vol 92 (10) ◽  
pp. 775-779 ◽  
Author(s):  
D. H. C. Herne ◽  
Wm. L. Putman
Keyword(s):  
Life History ◽  
New Species ◽  
North America ◽  
Life Histories ◽  
Fruit Trees ◽  
Extensive Study ◽  
Economic Importance ◽  
Eastern North America ◽  
Closely Related Species ◽  
A New Species

The ‘clover’ mite, Bryobia praetiosa Koch, has long been known to be a complex of closely related species or biological races differing greatly in host range, life-history, and habits. Morgan and Anderson (1957) reviewed the problem and described the form occurring on fruit trees in British Columbia as a new species, B. arborea, to be known as the brown mite, and these authors (Anderson and Morgan, 1958) also published a detailed study of the life-histories and habits of this species and of the true clover mite, B. praetiosa. Although the presence of Bryobia mites on fruit trees in Eastern North America, including Ontario, has long been recognized, they have seldom received more than casual mention and no extensive study of their biology in this area appears to have been undertaken. The species has little economic importance in Ontario (Putman and Herne, 1959).

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 Genomic evidence of a widespread southern distribution during the Last Glacial Maximum for two eastern North American hickory species

2017 ◽  
Author(s):  
Jordan B. Bemmels ◽  
Christopher W. Dick
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
North America ◽  
Last Glacial Maximum ◽  
Temperate Forest ◽  
Eastern North America ◽  
Carya Ovata ◽  
History Of ◽  
The Last Glacial Maximum ◽  
The Last Glacial

AimPhylogeographic studies of temperate forest taxa often infer complex histories involving population subdivision into distinct refugia during the Last Glacial Maximum (LGM). However, temperate forests may have been broadly distributed in southeastern North America during the LGM. We investigate genome-wide genetic structure in two widespread eastern North America tree species to determine if range expansion from a contiguous area or from genetically isolated refugia better explains the postglacial history of trees and forests from this region.LocationEastern North America (ENA).TaxaBitternut hickory (Carya cordiformis (Wangenh.) K.Koch) and shagbark hickory (Carya ovata (Mill.) K.Koch).MethodsGenetic diversity and differentiation indices were calculated from >1,000 nuclear SNP loci genotyped in ca. 180 individuals per species sampled across ENA. Genetic structure was investigated using principle component analysis and genetic clustering algorithms. As an additional tool for inference, areas of suitable habitat during the LGM were predicted using species distribution models (SDMs).ResultsPopulations across all latitudes showed similar levels of genetic diversity. Most genetic variation was weakly differentiated across ENA, with the exception of an outlier population of Carya ovata in Texas. Genetic structure in each species exhibited an isolation-by-distance pattern. SDMs predicted high LGM habitat suitability over much of the southeastern United States.Main conclusionsBoth hickory species likely survived the LGM in a large region of continuous habitat and recolonized northern areas in a single expanding front that encountered few migration barriers. More complex scenarios, such as forest refugia, need not be invoked to explain genetic structure. The genetically distinct Texas population of Carya ovata could represent a separate glacial refugium, but other explanations are possible. Relative to that of other temperate forest regions, the phylogeographic history of ENA may have been exceptionally simple, involving a northward range shift but without well defined refugia.

Genetic diversity of butternut (Juglans cinerea) and implications for conservation

2008 ◽  
Vol 38 (4) ◽  
pp. 899-907 ◽  
Author(s):  
Amy Ross-Davis ◽  
Michael Ostry ◽  
Keith E. Woeste
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Endangered Species ◽  
Isolation By Distance ◽  
Eastern North America ◽  
Native Range ◽  
Juglans Cinerea ◽  
Threatened And Endangered Species ◽  
Genetic Diversity And Structure

The management of threatened and endangered species can be improved by understanding their patterns of genetic diversity and structure. This paper presents the results of the first analysis of the population genetics of butternut ( Juglans cinerea L.) using nuclear microsatellites. Butternut once was an economically and ecologically valuable hardwood, but now its numbers are rapidly decreasing throughout its native range in eastern North America. By genotyping butternut trees (n = 157) from five populations at seven highly polymorphic loci, we determined that the remaining genetic diversity for the species is considerably higher than previously estimated (mean HE = 0.75). Populations were nearly genetically homogenous (FST = 0.025), with no evidence of isolation by distance. These results indicate that butternut retains a large amount of genetic diversity, and that it is not too late to implement strategies to conserve local butternut populations.

Using museum specimens to assess historical distribution and genetic diversity in an endangered butterfly

2012 ◽  
Vol 62 (3) ◽  
pp. 337-350 ◽  
Author(s):  
Emily V. Saarinen ◽  
Jaret C. Daniels
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Florida Keys ◽  
Suitable Habitat ◽  
Museum Specimens ◽  
Isolated Populations ◽  
Population Number ◽  
Metapopulation Structure ◽  
Historical Distribution ◽  
Key Largo

The Miami blue butterfly,Cyclargus thomasi bethunebakeri, is a state-endangered taxon in Florida and a candidate for federal listing. This once common butterfly saw a dramatic decline in population number and abundance in the 1970s and 1980s, but significant collections of individuals prior to this decline are deposited in natural history museums. Using museum specimens, we quantified the genetic diversity in a historical population present in Key Largo, Florida in 1940, 1960, and 1980. Genetic diversity was consistently high within this historical population, but diversity was observed to decrease over the decades sampled. A comparison of historical diversity from the Key Largo population with the extant populations on Bahia Honda State Park (BHSP) and Key West National Wildlife Refuge (KWNWR) revealed differences in allelic frequencies, but only minor differences in the overall number of alleles. The historical distribution of butterflies throughout the Florida Keys further suggests a metapopulation structure. This structure involved partially-isolated populations ofC. t. bethunebakerithat were loosely connected via gene flow and that underwent localized extinction and colonization events along the chain of suitable habitat in the Florida Keys. It appears that a “mini-metapopulation” currently exists on BHSP and KWNWR; structures that are similar to the historical metapopulation structure and distribution of populations on a larger scale. Knowledge of historical distribution helps to plan future reintroduction events with captive-bred butterflies. Additional populations of butterflies may represent undiscovered genetic diversity that, if appropriate, may be further incorporated into captive-breeding efforts.

A Genetic Analysis of Two Recently Described Peat Moss Species, Sphagnum atlanticum and S. bergianum (Sphagnaceae)

2009 ◽  
Vol 34 (1) ◽  
pp. 6-12 ◽  
Author(s):  
Blanka Shaw ◽  
Stefano Terracciano ◽  
A. Jonathan Shaw
Keyword(s):  
North America ◽  
Genetic Analysis ◽  
Microsatellite Loci ◽  
Related Species ◽  
Peat Moss ◽  
Eastern North America ◽  
Gene Pools ◽  
Similar Species ◽  
Closely Related Species ◽  
Moss Species

Microsatellite markers were used to test whether two recently described species of Sphagnum (Bryophyta), S. atlanticum R.E. Andrus and S. bergianum R.E. Andrus, represent distinct gene pools. The first species is considered endemic to eastern North America while the second species has been reported from Alaska and Newfoundland. The results indicate that S. atlanticum does not differ genetically from the closely related species, S. torreyanum, also restricted to eastern North America. In fact, some samples that are identical across all 15 microsatellite loci have been distinguished morphologically as these two species. Plants of S. bergianum from Alaska are closely related genetically to Alaskan plants of the similar species, S. subfulvum, whereas Newfoundland plants of S. bergianum are more closely related to Newfoundland plants of S. subfulvum. Alaskan versus Newfoundland plants of S. subfulvum s.l. (including S. bergianum) are differentiated at microsatellite loci. Another closely related species, S. subnitens, is distinct from S. subfulvum and S. bergianum. Sphagnum atlanticum is synonymized under S. torreyanum and S. bergianum is synonymized under S. subfulvum.

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