scholarly journals The Current Epidemic of the Barley Pathogen Ramularia collo-cygni Derives from a Population Expansion and Shows Global Admixture

2019 ◽  
Vol 109 (12) ◽  
pp. 2161-2168 ◽  
Author(s):  
Remco Stam ◽  
Hind Sghyer ◽  
Aurélien Tellier ◽  
Michael Hess ◽  
Ralph Hückelhoven
Keyword(s):  
Population Size ◽  
Yield Loss ◽  
Population Expansion ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Seed Transfer ◽  
Ramularia Leaf Spot ◽  
Global Spread ◽  
Sample Set ◽  
Important Disease

Ramularia leaf spot is becoming an ever-increasing problem in main barley-growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent Ramularia collo-cygni remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to what extent the pathogen has a sexual reproductive cycle. The teleomorph of R. collo-cygni has not been observed. To study the genetic diversity of R. collo-cygni and get more insights in its biology, we sequenced the genomes of 19 R. collo-cygni isolates from multiple geographic locations and diverse hosts. Nucleotide polymorphism analyses of all isolates shows that R. collo-cygni is genetically diverse worldwide, with little geographic or host specific differentiation. Next, we used two different methods to detect signals of recombination in our sample set. Both methods find putative recombination events, which indicate that sexual reproduction happens or has happened in the global R. collo-cygni population. Lastly, we used these data on recombination to perform historic population size analyses. These suggest that the effective population size of R. collo-cygni decreased during the domestication of barley and subsequently grew with the rise of agriculture. Our findings deepen our understanding of R. collo-cygni biology and can help us to understand the current epidemic. We discuss how our findings support possible global spread through seed transfer, and we highlight how recombination, clonal spreading, and lack of host specificity could amplify global epidemics of this increasingly important disease and suggest specific approaches to combat the pathogen.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

scholarly journals Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis

2008 ◽  
Vol 90 (1) ◽  
pp. 119-128 ◽  
Author(s):  
STEPHEN I. WRIGHT ◽  
NARDIN NANO ◽  
JOHN PAUL FOXE ◽  
VAQAAR-UN NISA DAR
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Likelihood Estimation ◽  
Composite Likelihood ◽  
Nuclear Genes ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Arabidopsis Lyrata ◽  
Tests Of Neutrality ◽  
Low Levels

SummaryCytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plant Arabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfing Arabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes in A. lyrata does not depart from the neutral expectation of 0·5. Similarly, the ratio of effective size in A. thaliana is close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles of A. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

scholarly journals Patterns of Nucleotide Diversity of theldpACircadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts

2012 ◽  
Vol 79 (5) ◽  
pp. 1516-1522 ◽  
Author(s):  
Ka Wai Ng ◽  
Stephen B. Pointing ◽  
Volodymyr Dvornyk
Keyword(s):  
Related Species ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Closely Related Species ◽  
Content Type ◽  
Population Sizes ◽  
Extreme Cold ◽  
Small Effective Population Size

ABSTRACTIn the circadian system of cyanobacteria, theldpAgene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted asSynechococcusspecies S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (FST= 0.2242) compared to those of species S1 (FSTbetween 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.

scholarly journals An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9939
Author(s):  
Jessica F. McLaughlin ◽  
Kevin Winker
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Population Level ◽  
Sample Sizes ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Single Nucleotide ◽  
Population Demographic

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

scholarly journals The demography of extinction in eastern North American birds

2021 ◽  
Vol 288 (1944) ◽  
pp. 20201945
Author(s):  
Brian Tilston Smith ◽  
Marcelo Gehara ◽  
Michael G. Harvey
Keyword(s):  
Population Size ◽  
Population Expansion ◽  
Species Traits ◽  
Small Population ◽  
Population Declines ◽  
Effective Population ◽  
Post Colonial ◽  
Extant Species ◽  
European Colonization ◽  
Demographic Patterns

Species are being lost at an unprecedented rate during the Anthropocene. Progress has been made in clarifying how species traits influence their propensity to go extinct, but the role historical demography plays in species loss or persistence is unclear. In eastern North America, five charismatic landbirds went extinct last century, and the causes of their extinctions have been heavily debated. Although these extinctions are most often attributed to post-colonial human activity, other factors such as declining ancestral populations prior to European colonization could have made these species particularly susceptible. We used population genomic data from these extinct birds and compared them with those from four codistributed extant species. We found extinct species harboured lower genetic diversity and effective population sizes than extant species, but both extinct and non-extinct birds had similar demographic histories of population expansion. These demographic patterns are consistent with population size changes associated with glacial–interglacial cycles. The lack of support for overall population declines during the Pleistocene corroborates the view that, although species that went extinct may have been vulnerable due to low diversity or small population size, their disappearance was driven by human activities in the Anthropocene.

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