scholarly journals Phantom histories of misspecified pasts

2020 ◽  
Author(s):  
Alexander Platt ◽  
Daniel N. Harris
Keyword(s):  
Natural Population ◽  
Population Decline ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Genome Sequences ◽  
Recent Population Expansion ◽  
A Genome ◽  
History Of

AbstractThe observation that even a tiny sample of genome sequences from a natural population contains a plethora of information about the history of the population has enticed researchers to use these data to fit complex demographic histories and make detailed inference about the changes a population has experienced through time. Unfortunately, the standard assumptions required to make these inferences are often violated by natural populations in such ways as to produce specious results. This paper examines two phenomena of particular concern: when a sample is drawn from a single sub-population of a larger meta-population these models infer a spurious recent population decline, and when a genome contains loci under weak or recessive purifying selection these models infer a spurious recent population expansion.

scholarly journals Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

2002 ◽  
Vol 80 (3) ◽  
pp. 163-175 ◽  
Author(s):  
STEPHEN W. SCHAEFFER
Keyword(s):  
Negative Selection ◽  
Genome Rearrangement ◽  
Rare Variants ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Sequence Length ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Indel Variation

Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.

Signatures of mito-nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe

Parasitology ◽  
2017 ◽  
Vol 144 (13) ◽  
pp. 1752-1762 ◽  
Author(s):  
SCOTT P. LAWTON ◽  
LAUREN I. BOWEN ◽  
AIDAN M. EMERY ◽  
GÁBOR MAJOROS
Keyword(s):  
Evolutionary History ◽  
Molecular Diversity ◽  
Population Expansion ◽  
Its Sequences ◽  
Cox1 Gene ◽  
Internal Transcribed Spacer Region ◽  
Recent Population Expansion ◽  
Haplotype Frequencies ◽  
History Of ◽  
Low Levels

SUMMARYHigh levels of molecular diversity were identified in mitochondrial cytochrome c oxidase (cox1) gene sequences of Schistosoma turkestanicum from Hungary. These cox1 sequences were all specific to Hungary which contrasted with the low levels of diversity seen in the nuclear internal transcribed spacer region (ITS) sequences, the majority of which were shared between China and Iran isolates. Measures of within and between host molecular variation within S. turkestanicum showed there to be substantial differences in molecular diversity, with cox1 being significantly more diverse than the ITS. Measures of haplotype frequencies revealed that each host contained its own subpopulation of genetically unique parasites with significant levels of differentiation. Pairwise mismatch analysis of cox1 sequences indicated S. turkestanicum populations to have a bimodal pairwise difference distribution and to be stable unlike the ITS sequences, which appeared to have undergone a recent population expansion event. Positive selection was also detected in the cox1 sequences, and biochemical modelling of the resulting protein illustrated significant mutational events causing an alteration to the isoelectric point of the cox1 protein, potentially altering metabolism. The evolutionary signature from the cox1 indicates local adaptation and long establishment of S. turkestanicum in Hungary with continual introgression of nuclear genes from Asian isolates. These processes have led to the occurrence of mito-nuclear discordance in a schistosome population

scholarly journals Impact of Host Resistance to Tomato Spotted Wilt Orthotospovirus in Peanut Cultivars on Virus Population Genetics and Thrips Fitness

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1418
Author(s):  
Pin-Chu Lai ◽  
Mark R. Abney ◽  
Sudeep Bag ◽  
Albert K. Culbreath ◽  
Rajagopalbabu Srinivasan
Keyword(s):  
Population Genetics ◽  
Host Resistance ◽  
Selection Pressure ◽  
Phylogenetic Trees ◽  
Population Expansion ◽  
Purifying Selection ◽  
Recent Population Expansion ◽  
Resistant Cultivars ◽  
Tomato Spotted Wilt ◽  
Peanut Cultivars

Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) is a major constraint to peanut production in the southeastern United States. Peanut cultivars with resistance to TSWV have been widely used for over twenty years. Intensive usage of resistant cultivars has raised concerns about possible selection pressure against TSWV and a likelihood of resistance breakdown. Population genetics of TSWV isolates collected from cultivars with varying levels of TSWV resistance was investigated using five TSWV genes. Phylogenetic trees of genes did not indicate host resistance-based clustering of TSWV isolates. Genetic variation in TSWV isolates and neutrality tests suggested recent population expansion. Mutation and purifying selection seem to be the major forces driving TSWV evolution. Positive selection was found in N and RdRp genes but was not influenced by TSWV resistance. Population differentiation occurred between isolates collected from 1998 and 2010 and from 2016 to 2019 but not between isolates from susceptible and resistant cultivars. Evaluated TSWV-resistant cultivars differed, albeit not substantially, in their susceptibility to thrips. Thrips oviposition was reduced, and development was delayed in some cultivars. Overall, no evidence was found to support exertion of selection pressure on TSWV by host resistance in peanut cultivars, and some cultivars differentially affected thrips fitness than others.

scholarly journals Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 338 ◽  
Author(s):  
Xue Zhang ◽  
Yuan-Huan Liu ◽  
Yue-Hua Wang ◽  
Shi-Kang Shen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Population Decline ◽  
Population Expansion ◽  
Distribution Models ◽  
Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

scholarly journals A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

mSphere ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Tsuyoshi Sekizuka ◽  
Kentaro Itokawa ◽  
Masanori Hashino ◽  
Tetsuro Kawano-Sugaya ◽  
Rina Tanaka ◽  
...  
Keyword(s):  
Network Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Haplotype Network ◽  
Epidemiological Surveillance ◽  
Genome Sequences ◽  
First Case ◽  
Field Investigations ◽  
A Genome ◽  
Reverse Transcription Quantitative Pcr ◽  
History Of

ABSTRACT After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries. IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

scholarly journals Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammad Reza Ashrafzadeh ◽  
Rasoul Khosravi ◽  
Carlos Fernandes ◽  
Cecilia Aguayo ◽  
Zoltán Bagi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Demographic History ◽  
Population Expansion ◽  
Game Species ◽  
Recent Population Expansion ◽  
Biogeographic Patterns ◽  
Clustering Model ◽  
History Of ◽  
Common Pheasant ◽  
The Common

AbstractThe common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.

scholarly journals Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

2021 ◽  
Vol 12 ◽  
Author(s):  
Lourdes Valdez ◽  
Guillermo D’Elía
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Population Expansion ◽  
Principal Component ◽  
Tierra Del Fuego ◽  
Local Fauna ◽  
Recent Population Expansion ◽  
Genetic Groups ◽  
History Of ◽  
Species Specific

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

scholarly journals Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites

2018 ◽  
Vol 115 (36) ◽  
pp. E8450-E8459 ◽  
Author(s):  
Dorothy E. Loy ◽  
Lindsey J. Plenderleith ◽  
Sesh A. Sundararaman ◽  
Weimin Liu ◽  
Jakub Gruszczyk ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Sequence Data ◽  
Population Expansion ◽  
Purifying Selection ◽  
Nucleotide Polymorphisms ◽  
Binding Studies ◽  
Frequency Spectra ◽  
Genome Wide ◽  
History Of ◽  
Human Plasmodium

Wild-living African apes are endemically infected with parasites that are closely related to human Plasmodium vivax, a leading cause of malaria outside Africa. This finding suggests that the origin of P. vivax was in Africa, even though the parasite is now rare in humans there. To elucidate the emergence of human P. vivax and its relationship to the ape parasites, we analyzed genome sequence data of P. vivax strains infecting six chimpanzees and one gorilla from Cameroon, Gabon, and Côte d’Ivoire. We found that ape and human parasites share nearly identical core genomes, differing by only 2% of coding sequences. However, compared with the ape parasites, human strains of P. vivax exhibit about 10-fold less diversity and have a relative excess of nonsynonymous nucleotide polymorphisms, with site-frequency spectra suggesting they are subject to greatly relaxed purifying selection. These data suggest that human P. vivax has undergone an extreme bottleneck, followed by rapid population expansion. Investigating potential host-specificity determinants, we found that ape P. vivax parasites encode intact orthologs of three reticulocyte-binding protein genes (rbp2d, rbp2e, and rbp3), which are pseudogenes in all human P. vivax strains. However, binding studies of recombinant RBP2e and RBP3 proteins to human, chimpanzee, and gorilla erythrocytes revealed no evidence of host-specific barriers to red blood cell invasion. These data suggest that, from an ancient stock of P. vivax parasites capable of infecting both humans and apes, a severely bottlenecked lineage emerged out of Africa and underwent rapid population growth as it spread globally.

scholarly journals A genome epidemiological study of SARS-CoV-2 introduction into Japan

2020 ◽  
Author(s):  
Tsuyoshi Sekizuka ◽  
Kentaro Itokawa ◽  
Masanori Hashino ◽  
Tetsuro Kawano-Sugaya ◽  
Rina Tanaka ◽  
...  
Keyword(s):  
Network Analysis ◽  
Haplotype Network ◽  
Epidemiological Surveillance ◽  
Genome Sequences ◽  
Chain Reaction ◽  
First Case ◽  
A Genome ◽  
History Of ◽  
Polymerase Chain ◽  
National Emergency

AbstractBackgroundAfter the first case of COVID-19 in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases appeared until early April, many with unclear infection routes exhibiting no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases until early April and characterise the genealogical networks to demonstrate possible routes of spread in Japan.MethodsNasopharyngeal specimens were collected from patients and a quantitative reverse transcription polymerase chain reaction testing for SARS-CoV-2 was performed. Positive RNA samples were subjected whole genome sequencing and a haplotype network analysis was performed.FindingsSome of the primary clusters identified during January and February in Japan directly descended from Wuhan-Hu-1-related isolates in China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that COVID-19 cases from late March through early April may have caused an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. National self-restraint during February was effective in mitigating the COVID-19 spread, but late action on stopping immigration and declaring national emergency in Japan might be involved in the later increase in cases.InterpretationGenome surveillance suggested that at least two distinct SARS-CoV-2 introductions from China and other countries occurred.FundingJapan Agency for Medical Research and Development.

Sign in / Sign up

Export Citation Format

Share Document