POPULATION GENETICS OF COASTAL AND ESTUARINE INVERTEBRATES: DOES LARVAL BEHAVIOR INFLUENCE POPULATION STRUCTURE?

1982 ◽  
pp. 537-551 ◽  
Author(s):  
Ronald S. Burton ◽  
Marcus W. Feldman
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Larval Behavior

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Reply to the comment by Morales et al. on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

2021 ◽  
pp. 423-432
Author(s):  
C.L. Lausen ◽  
Michael F. Proctor ◽  
David Paetkau ◽  
David W. Nagorsen ◽  
Purnima Govindarajulu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Single Species ◽  
Distinct Species ◽  
Background Information ◽  
Distribution Data ◽  
Supporting Evidence ◽  
Post Mortem ◽  
The Impact ◽  
New Evidence

A.E. Morales et al. (2021. Can. J. Zool. 99(5): 415–422) provided no new evidence to alter the conclusions of C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279). We present background information, relevant comparisons, and clarification of analyses to further strengthen our conclusions. The genesis of the original “evotis–keenii” study in British Columbia (Canada) was to differentiate Myotis keenii (Merriam, 1895) (Keen’s myotis), with one of the smallest North American bat distributions, from sympatric Myotis evotis (H. Allen, 1864) (long-eared myotis), using something other than the suggested post-mortem skull size comparison, but no differentiating trait could be found, leading to the molecular genetics examination of C.L. Lausen et al. (2019). We present cumulative data that rejects the 1979 hypothesis of M. keenii as a distinct species. A.E. Morales et al. (2021) inaccurately portray C.L. Lausen et al.’s (2019) question and results; present inaccurate morphological and outdated distribution data; overstate the impact of homoplasy without supporting evidence; and misinterpret evidence of population structure.

scholarly journals Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 Diabetes

2010 ◽  
Vol 27 (11) ◽  
pp. 2555-2566 ◽  
Author(s):  
M. Fumagalli ◽  
R. Cagliani ◽  
S. Riva ◽  
U. Pozzoli ◽  
M. Biasin ◽  
...  
Keyword(s):  
Population Genetics ◽  
Type 1 Diabetes ◽  
Population Structure ◽  
Ancient Population ◽  
Local Selection

scholarly journals Population genetics of immune-related multilocus copy number variation in Native Americans

2017 ◽  
Vol 14 (128) ◽  
pp. 20170057 ◽  
Author(s):  
Luciana W. Zuccherato ◽  
Silvana Schneider ◽  
Eduardo Tarazona-Santos ◽  
Robert J. Hardwick ◽  
Douglas E. Berg ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Native American ◽  
Native Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genomic Variation ◽  
Population Subdivision ◽  
Nucleotide Polymorphisms ◽  
Number Variation

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f , which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1 , FCGR3A , FCGR3B and FCGR2C ) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

scholarly journals Scaling probabilistic models of genetic variation to millions of humans

2014 ◽  
Author(s):  
Prem Gopalan ◽  
Wei Hao ◽  
David M. Blei ◽  
John D. Storey
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Genetic Variation ◽  
Probabilistic Models ◽  
Simulated Data ◽  
Genomic Data ◽  
Human Populations ◽  
Data Sets ◽  
Complex Population ◽  
Simulated Data Sets

One of the major goals of population genetics is to quantitatively understand variation of genetic polymorphisms among individuals. To this end, researchers have developed sophisticated statistical methods to capture the complex population structure that underlies observed genotypes in humans, and such methods have been effective for analyzing modestly sized genomic data sets. However, the number of genotyped humans has grown significantly in recent years, and it is accelerating. In aggregate about 1M individuals have been genotyped to date. Analyzing these data will bring us closer to a nearly complete picture of human genetic variation; but existing methods for population genetics analysis do not scale to data of this size. To solve this problem we developed TeraStructure. TeraStructure is a new algorithm to fit Bayesian models of genetic variation in human populations on tera-sample-sized data sets (1012observed genotypes, e.g., 1M individuals at 1M SNPs). It is a principled approach to Bayesian inference that iterates between subsampling locations of the genome and updating an estimate of the latent population structure of the individuals. On data sets of up to 2K individuals, TeraStructure matches the existing state of the art in terms of both speed and accuracy. On simulated data sets of up to 10K individuals, TeraStructure is twice as fast as existing methods and has higher accuracy in recovering the latent population structure. On genomic data simulated at the tera-sample-size scales, TeraStructure continues to be accurate and is the only method that can complete its analysis.

scholarly journals Isolation-By-Distance-and-Time in a stepping-stone model

2015 ◽  
Author(s):  
Nicolas Duforet-Frebourg ◽  
Montgomery Slatkin
Keyword(s):  
Principal Component Analysis ◽  
Population Genetics ◽  
Population Structure ◽  
Isolation By Distance ◽  
Principal Component ◽  
Joint Effect ◽  
Stepping Stone ◽  
Ancient Times ◽  
The Impact ◽  
Stepping Stone Model

With the great advances in ancient DNA extraction, population genetics data are now made of geographically separated individuals from both present and ancient times. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping--stone model, we develop the theory of Isolation by Distance and Time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present in the data, and investigate the impact of edge effects with forward-in-time simulations. We also derive results about coalescent times in circular/toroidal models. As one of the most common way to investigate population structure is to apply principal component analysis, we evaluate the impact of this theory on plots of principal components. Our results demonstrate that time between samples is a non-negligible factor that requires new attention in population genetics.

Epidemic population structure of clinical Klebsiella aerogenes inferred by multilocus sequence typing

2019 ◽  
Author(s):  
Sheng Chen ◽  
Yu Wang ◽  
Lijun Zeng ◽  
Wenbo Luo ◽  
Wei Feng ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Homologous Recombination ◽  
Key Words ◽  
Multilocus Sequence Typing ◽  
Bacterial Population ◽  
Purifying Selection ◽  
Klebsiella Aerogenes ◽  
Sequence Types

Abstract Background: Multilocus sequence typing (MLST) act as an accurate approach to characterize bacterial population genetics, phylogeny and epidemiology, and has not yet been applied to Klebsiella aerogenes. Results: A MLST scheme was established for a collection of 213 isolates of K. aerogenes. These strains exhibited considerable sequence diversity under purifying selection, and could be assigned into 135 sequence types, which were further divided into 8 clonal complexes and a lot of doubletons and singletons scatterred in the population snapshot. Five separately clustering lineages were presented in the population, which displayed evident homologous recombination occurred within and across lineages, with a tendency of linkage disequilibrium. Conclusions: K. aerogenes shows an epidemic population structure displaying high levels of recombination occurring more frequently than point mutation. Key words: Klebsiella aerogenes; multilocus sequence typing; sequence types; purifying selection; linkage disequilibrium; population structure

scholarly journals SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Abebe A. Fola ◽  
Eline Kattenberg ◽  
Zahra Razook ◽  
Dulcie Lautu-Gumal ◽  
Stuart Lee ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Plasmodium Vivax ◽  
Malaria Transmission ◽  
Snp Markers ◽  
North Coast ◽  
High Quality ◽  
Catchment Areas ◽  
The Impact

Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since ‘universal’ barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. Methods Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. Results From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56–7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. Conclusions High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.

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