scholarly journals Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.

2021 ◽  
Author(s):  
Graham John Etherington ◽  
Adam Ciezarek ◽  
Rebecca Shaw ◽  
Johan Michaux ◽  
Elizabeth Croose ◽  
...  
Keyword(s):  
Great Britain ◽  
Cognitive Function ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Population Recovery ◽  
Ural Mountains ◽  
Mustela Putorius ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as pure polecats. We quantify this introgression and find introgressed genes under selection that may assist in cognitive function and sight.

Introgression v1

2021 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Great Britain ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Mustela Putorius ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

GATK Nuclear variant discovery and consensus assembly v1

2020 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Great Britain ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Mustela Putorius ◽  
Variant Discovery ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

scholarly journals Diets of European polecat Mustela putorius in Great Britain during fifty years of population recovery

2020 ◽  
Vol 65 (2) ◽  
pp. 181-190
Author(s):  
Katherine A. Sainsbury ◽  
Richard F. Shore ◽  
Henry Schofield ◽  
Elizabeth Croose ◽  
Georg Hantke ◽  
...  
Keyword(s):  
Great Britain ◽  
Population Recovery ◽  
Mustela Putorius

Age-specific growth, survival, and population dynamics of female Australian fur seals

2009 ◽  
Vol 87 (10) ◽  
pp. 902-911 ◽  
Author(s):  
J. Gibbens ◽  
J.P.Y. Arnould
Keyword(s):  
Survival Rates ◽  
Habitat Type ◽  
Recent Change ◽  
Body Growth ◽  
Population Increase ◽  
Adult Survival ◽  
Population Recovery ◽  
Foraging Mode ◽  
Sea Lions ◽  
Fur Seals

Postsealing population recovery rates of fur seals and sea lions have differed markedly, perhaps owing to habitat type. Australian fur seals ( Arctocephalus pusillus doriferus Wood Jones, 1925) employ a benthic foraging mode similar to sea lions, and have exhibited similarly slow population recovery. Nonetheless, the population doubled in recent decades, suggesting a recent change in demographic rates. In the present study, the frequency and size of known-age females (n = 297) were used to create body growth and survivorship models. These were compared with models obtained in the 1970s before the recent population increase. Body growth, which is relatively rapid in comparison to other fur seal species, remains unchanged since the 1970s, suggesting that density-dependent effects are absent despite the population increases. Adult survival rates (weighted mean: 0.885) have increased greatly since the 1970s and are the likely mechanism of the recent increases. Total population abundance was estimated to be 4.5 times that of pups. Australian fur seals display high survivorship, rapid body growth, low fecundity, and low population growth rates; all are characteristics typical of benthic foraging sea lions rather than other fur seals.

scholarly journals Multiplex SARS-CoV-2 Genotyping PCR for Population-Level Variant Screening and Epidemiologic Surveillance

2021 ◽  
Author(s):  
Hannah Wang ◽  
Jacob A. Miller ◽  
Michelle Verghese ◽  
Mamdouh Sibai ◽  
Daniel Solis ◽  
...  
Keyword(s):  
Public Health ◽  
Nucleic Acid ◽  
Whole Genome Sequencing ◽  
San Francisco ◽  
Genome Sequencing ◽  
High Throughput ◽  
Population Level ◽  
Nucleic Acid Amplification ◽  
Whole Genome ◽  
Epidemiologic Surveillance

ABSTRACTBackgroundEmergence of SARS-CoV-2 variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a spike genotyping nucleic acid amplification test (NAAT) could facilitate high-throughput variant surveillance.MethodsWe designed and analytically validated a one-step multiplex allele-specific reverse transcriptase polymerase chain reaction (RT-qPCR) to detect three non-synonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2 positive specimens from our San Francisco Bay Area population.ResultsBetween December 1, 2020 and March 1, 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K+N501Y mutations. The assay had near-perfect (98-100%) concordance with whole-genome sequencing in a validation subset of 229 specimens, and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed rapid emergence of L452R in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021.ConclusionsWe developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.Summary / Key PointsEmergence of SARS-CoV-2 variants with concerning phenotypes is of public health interest. We developed a multiplex genotyping RT-qPCR to rapidly detect L452R, E484K, and N501Y with high sequencing concordance. This high-throughput alternative to resource-intensive sequencing enabled surveillance of L452R emergence.

scholarly journals Trajectories of Cognitive and Motor Function Between Ages 45 and 90 Years: A Population-Based Study

2020 ◽  
Author(s):  
Kimberly D van der Willik ◽  
Silvan Licher ◽  
Elisabeth J Vinke ◽  
Maria J Knol ◽  
Sirwan K L Darweesh ◽  
...  
Keyword(s):  
Cognitive Function ◽  
Motor Function ◽  
Population Level ◽  
Population Based ◽  
Community Dwelling ◽  
Age Difference ◽  
Population Based Study ◽  
Motor Tests ◽  
Rate Of Decline

Abstract Background To establish trajectories of cognitive and motor function, and to determine the sequence of change across individual tests in community-dwelling individuals aged 45–90 years. Method Between 1997 and 2016, we repeatedly assessed cognitive function with 5 tests in 9514 participants aged 45–90 years from the population-based Rotterdam Study. Between 1999 and 2016, we measured motor function with 3 tests in 8297 participants. All participants were free from dementia, stroke, and parkinsonism. We assessed overall and education-specific cognitive and motor trajectories using linear mixed models with age as time scale. Next, we determined the sequence of change across individual tests. Results The number of assessments per participant ranged between 1 and 6 (mean interval, years [SD]: 5.1 [1.4]) for cognitive function, and 1 and 4 (5.4 [1.4]) for motor function. Cognitive and motor trajectories declined linearly between ages 45 and 65 years, followed by steeper declines after ages 65–70 years. Lower educated participants had lower cognitive function at age 45 years (baseline), and declined faster on most cognitive, but not on motor tests than higher educated participants. Up to a 25-year age difference between the fastest and slowest declining test scores was observed. Conclusions On a population-level, cognitive and motor function decline similarly. Compared to higher educated individuals, lower educated individuals had lower cognitive function at baseline, and a faster rate of decline thereafter. These educational-effects were not seen for motor function. These findings benefit the understanding of the natural course of cognitive and motor function during aging, and highlight the role of education in the preservation of cognitive but not motor function.

A bounded growth population subjected to emigrations due to population pressure

1981 ◽  
Vol 18 (03) ◽  
pp. 571-582 ◽  
Author(s):  
A. C. Trajstman
Keyword(s):  
Size Distribution ◽  
Population Level ◽  
Population Pressure ◽  
Population Increase ◽  
Time To Extinction ◽  
Mean Time To Extinction ◽  
The Mean ◽  
The Times ◽  
Negative Exponential ◽  
Mean Time

A model is presented for a bounded growth population subjected to random-sized emigrations that occur due to population pressure. The deterministic growth component examined in detail is defined by a Prendiville process. Results are obtained for the times between emigration events and for the population increase between emigrations. Some information is obtained about the mean time to extinction and also for the mean population level when the emigration-size distribution is negative exponential.

Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California

2007 ◽  
Vol 64 (1) ◽  
pp. 30-42 ◽  
Author(s):  
Katherine A Bucklin ◽  
Michael A Banks ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Random Mating ◽  
Oncorhynchus Kisutch ◽  
Legal Protection ◽  
Population Level ◽  
Population Subdivision ◽  
Minimal Impact ◽  
Low Genetic Diversity ◽  
Microsatellite Dna Markers

California coho salmon (Oncorhynchus kisutch) are under legal protection owing to significant declines in abundance over the last decades. Previously, California coho salmon were characterized as having low genetic diversity and weak population subdivision, attributable potentially to homogenization by out-of-basin hatchery releases. Here, diversity at seven highly polymorphic microsatellite DNA markers is assessed within and among 32 collections of coho salmon from 16 California watersheds. In 71% of local populations, genotypic composition deviates significantly from that expected under the assumption of random mating. We develop and apply methods to adjust for two potential causes of deviation from random mating expectations: (i) Wahlund effects, owing to heterogeneous collections of individuals, and (ii) the "Allendorf–Phelp's effect", owing to closely related juveniles in samples. Such population-level "adjustments" reduce within-region and increase among-region variance; after adjustment, we find strong concordance of genetic and geographic distances. We conclude that stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding.

A bounded growth population subjected to emigrations due to population pressure

1981 ◽  
Vol 18 (3) ◽  
pp. 571-582 ◽  
Author(s):  
A. C. Trajstman
Keyword(s):  
Size Distribution ◽  
Population Level ◽  
Population Pressure ◽  
Population Increase ◽  
Time To Extinction ◽  
Mean Time To Extinction ◽  
The Mean ◽  
The Times ◽  
Negative Exponential ◽  
Mean Time

A model is presented for a bounded growth population subjected to random-sized emigrations that occur due to population pressure.The deterministic growth component examined in detail is defined by a Prendiville process. Results are obtained for the times between emigration events and for the population increase between emigrations. Some information is obtained about the mean time to extinction and also for the mean population level when the emigration-size distribution is negative exponential.

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