Progress and Prospects of Population Genomics of North American Hardwoods

2021 ◽  
Author(s):  
Oliver Gailing ◽  
Margaret Staton ◽  
Scott E. Schlarbaum ◽  
Mark V. Coggeshall ◽  
Jeanne Romero-Severson ◽  
...  
Keyword(s):  
North American ◽  
Population Genomics

scholarly journals Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly

2020 ◽  
Author(s):  
Hollie A Johnson ◽  
Eric B Rondeau ◽  
David R Minkley ◽  
Jong S Leong ◽  
Joanne Whitehead ◽  
...  
Keyword(s):  
Genome Assembly ◽  
North American ◽  
Population Genomics ◽  
Northern Pike ◽  
Ice Age ◽  
River Drainage ◽  
Yukon River ◽  
Long Read ◽  
Tajima’S D ◽  
Chromosome Level

AbstractWe present a chromosome-level, long-read genome assembly as a reference for northern pike (Esox lucius) where 97.5% of the genome is chromosome-anchored and N50 falls at 37.5 Mb. Whole-genome resequencing was genotyped using this assembly for 47 northern pike representing six North American populations from Alaska to New Jersey. We discovered that a disproportionate frequency of genetic polymorphism exists among populations east and west of the North American Continental Divide (NACD), indicating reproductive isolation across this barrier. Genome-wide analysis of heterozygous SNP density revealed a remarkable lack of genetic variation with 1 polymorphic site every 6.3kb in the Yukon River drainage and one every 16.5kb east of the NACD. Observed heterozygosity (Ho), nucleotide diversity (π), and Tajima’s D are depressed in populations east of the NACD (east vs. west: Ho: 0.092 vs 0.31; π: 0.092 vs 0.28; Tajima’s D: -1.61 vs -0.47). We confirm the presence of the master sex determining (MSD) gene, amhby, in the Yukon River drainage and in an invasive population in British Columbia and confirm its absence in populations east of the NACD. We also describe an Alaskan population where amhby is present but not associated with male gender determination. Our results support that northern pike originally colonized North America through Beringia, that Alaska provided an unglaciated refugium for northern pike during the last ice age, and southeast of the NACD was colonized by a small founding population(s) that lost amhby.

scholarly journals Estimating movement rates between Eurasian and North American birds that are vectors of avian influenza (AI)

2021 ◽  
Author(s):  
Fern Spaulding ◽  
Jessica F. McLaughlin ◽  
Travis C. Glenn ◽  
Kevin Winker
Keyword(s):  
Gene Flow ◽  
Relative Risk ◽  
Avian Influenza ◽  
North American ◽  
Population Genomics ◽  
Effective Population ◽  
Anas Acuta ◽  
Movement Rates ◽  
Census Size

Avian influenza (AI) is an emerging zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene flow, between Eurasian and North American waterbird populations to obtain bidirectional baseline rates of the intercontinental movements of these AI hosts. We used population genomics and coalescent-based demographic models to obtain these gene-flow-based movement estimates. Inferred rates of movement between these populations varies greatly among species. Within dabbling ducks, gene flow, relative to effective population size, varies from ~3-24 individuals/generation between Eurasian and American wigeons (Mareca penelope — M. americana) to ~100-300 individuals/generation between continental populations of northern pintails (Anas acuta). These are evolutionary long-term averages and provide a solid foundation for understanding the relative risks of each of these host species in potential intercontinental AI movements. We scale these values to census size for evaluation in that context. In addition to being AI hosts, many of these species are also important in the subsistence diets of Alaskans, increasing the risk of direct bird-to-human exposure to Eurasian-origin AI virus. We contrast species-specific rates of intercontinental movements with the importance of each species in Alaskan diets to understand the relative risk of these taxa to humans. Greater scaup (Aythya marila), mallard (Anas platyrhynchos), and northern pintail (Anas acuta) were the top three species presenting the highest risks for intercontinental AI movement both within the natural system and through exposure to subsistence hunters. These directly comparable, species-based intercontinental movement rates and relative risk rankings should help in modeling, monitoring, and mitigating the impacts of intercontinental host and AI movements.

scholarly journals Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

2020 ◽  
Vol 33 (2) ◽  
pp. 189-199 ◽  
Author(s):  
J. F. Tabima ◽  
K. L. Søndreli ◽  
S. Keriö ◽  
N. Feau ◽  
M. L. Sakalidis ◽  
...  
Keyword(s):  
United States ◽  
British Columbia ◽  
North America ◽  
North American ◽  
Plant Pathogens ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Plant Domestication ◽  
North American Population ◽  
The North

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

scholarly journals Population genomics of a reindeer lichen species from North American lichen woodlands

2021 ◽  
Vol 108 (1) ◽  
pp. 159-171 ◽  
Author(s):  
Marta Alonso‐García ◽  
Felix Grewe ◽  
Serge Payette ◽  
Juan Carlos Villarreal A.
Keyword(s):  
North American ◽  
Population Genomics ◽  
Lichen Species ◽  
Reindeer Lichen

Adaptation of the Connected Speech Test: Rerecording and Passage Equivalency

2020 ◽  
Vol 29 (2) ◽  
pp. 259-264 ◽  
Author(s):  
Hasan K. Saleh ◽  
Paula Folkeard ◽  
Ewan Macpherson ◽  
Susan Scollie
Keyword(s):  
Speech Perception ◽  
North American ◽  
First Language ◽  
Intraclass Correlation ◽  
Normal Hearing ◽  
Connected Speech ◽  
Internal Reliability ◽  
Speech Test ◽  
The Mean ◽  
Unit Standard

Purpose The original Connected Speech Test (CST; Cox et al., 1987) is a well-regarded and often utilized speech perception test. The aim of this study was to develop a new version of the CST using a neutral North American accent and to assess the use of this updated CST on participants with normal hearing. Method A female English speaker was recruited to read the original CST passages, which were recorded as the new CST stimuli. A study was designed to assess the newly recorded CST passages' equivalence and conduct normalization. The study included 19 Western University students (11 females and eight males) with normal hearing and with English as a first language. Results Raw scores for the 48 tested passages were converted to rationalized arcsine units, and average passage scores more than 1 rationalized arcsine unit standard deviation from the mean were excluded. The internal reliability of the 32 remaining passages was assessed, and the two-way random effects intraclass correlation was .944. Conclusion The aim of our study was to create new CST stimuli with a more general North American accent in order to minimize accent effects on the speech perception scores. The study resulted in 32 passages of equivalent difficulty for listeners with normal hearing.

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