Environmental Patterns Are Imposed on the Population Structure ofEscherichia coliafter Fecal Deposition

ABSTRACTThe intestinal microbeEscherichia coliis subject to fecal deposition in secondary habitats, where it persists transiently, allowing for the opportunity to colonize new hosts. Selection in the secondary habitat can be postulated, but its impact on the genomic diversity ofE. coliis unknown. Environmental selective pressure on extrahostE. colican be revealed by landscape genetic analysis, which examines the influences of dispersal processes, landscape features, and the environment on the spatiotemporal distribution of genes in natural populations. We conducted multilocus sequence analysis of 353E. coliisolates from soil and fecal samples obtained in a recreational meadow to examine the ecological processes controlling their distributions. Soil isolates, as a group, were not genetically distinct from fecal isolates, with only 0.8% of genetic variation and no fixed mutations attributed to the isolate source. Analysis of the landscape genetic structure ofE. colipopulations showed a patchy spatial structure consistent with patterns of fecal deposition. Controlling for the spatial pattern made it possible to detect environmental gradients of pH, moisture, and organic matter corresponding to the genetic structure ofE. coliin soil. Ecological distinctions amongE. colisubpopulations (i.e.,E. colireference collection [ECOR] groups) contributed to variation in subpopulation distributions. Therefore, while fecal deposition is the major predictor ofE. colidistributions on the field scale, selection imposed by the soil environment has a significant impact onE. colipopulation structure and potentially amplifies the occasional introduction of stress-tolerant strains to new host individuals by transmission through water or food.

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Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

10.1101/2020.10.08.331140 ◽

2020 ◽

Author(s):

Brenda G. Díaz ◽

Maria I. Zucchi ◽

Alessandro. Alves-Pereira ◽

Caléo P. de Almeida ◽

Aline C. L. Moraes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Structure ◽

Genetic Relationships ◽

Geographical Area ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Productive Capacity ◽

Snp Analysis ◽

Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

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Genetic structure of natterjack toad (Epidalea calamita) populations in Flanders, Belgium, and its implications for conservation

Amphibia-Reptilia ◽

10.1163/15685381-17000181 ◽

2019 ◽

Vol 40 (2) ◽

pp. 193-205

Author(s):

Joke Maes ◽

Arend Raoul Van Oosten ◽

Natalie Van Houtte ◽

Erik Matthysen

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Habitat Management ◽

Natural Populations ◽

Conservation Priorities ◽

Evolutionary Potential ◽

Isolated Populations ◽

Genetic Population ◽

Wide Range ◽

Epidalea Calamita

Abstract Unique evolutionary potential could be lost when a population goes extinct or when individuals are translocated to other existing populations. Therefore, in order to identify priorities and to predict the efficiency and consequences of conservation actions, information is needed on the genetic structure of natural populations. In the urbanized and diverse landscapes of Flanders, Belgium, natterjack toad (Epidalea calamita) populations have been declining over the last decades. Therefore, this species is subjected to a wide range of different types of conservation measures (e.g. habitat management, corridor development, translocations). However, more information is needed on its genetic population structure. In this study, we sampled egg clutches from six populations and studied their genetic structure with six microsatellite markers. In total, 184 samples from 99 different egg strings were genotyped. Observed heterozygosity was generally high, even for the small and isolated populations (overall mean HO = 0.43). The weak clustering by the Bayesian analyses (STRUCTURE, Adegenet and BAPS) does not allow us to make strong conclusions on the population structure. However, the significant ΦST values between the populations underline the importance of genetic information when conservation priorities are discussed. Unique evolutionary potential could be lost when one or more natterjack toad populations would go extinct, and translocation of individuals to other existing populations should be considered with caution.

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Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species

PLoS ONE ◽

10.1371/journal.pone.0241025 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0241025

Author(s):

Brenda Gabriela Díaz ◽

Maria Imaculada Zucchi ◽

Alessandro Alves‐Pereira ◽

Caléo Panhoca de Almeida ◽

Aline Costa Lima Moraes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Structure ◽

Genetic Relationships ◽

Geographical Area ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Productive Capacity ◽

Snp Analysis ◽

Genetic Population

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

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Evolutionary and ecological processes influencing chemical defense variation in an aposematic and mimetic Heliconius butterfly

PeerJ ◽

10.7717/peerj.11523 ◽

2021 ◽

Vol 9 ◽

pp. e11523

Author(s):

Anniina L. K. Mattila ◽

Chris D. Jiggins ◽

Øystein H. Opedal ◽

Gabriela Montejo-Kovacevich ◽

Érika C. Pinheiro de castro ◽

...

Keyword(s):

Intraspecific Variation ◽

Adaptive Evolution ◽

Evolutionary Dynamics ◽

De Novo ◽

Environmental Gradients ◽

Natural Populations ◽

Common Garden ◽

Skewed Distribution ◽

Evolutionary Potential ◽

Ecological Processes

Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. Cyanogenic Heliconius butterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation in de novo biosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations of Heliconius erato along environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles of H. erato from geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems.

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Genetic structure in natural populations of flukes and snails: a practical approach and review

Parasitology ◽

10.1017/s0031182001007715 ◽

2001 ◽

Vol 123 (7) ◽

pp. 27-40 ◽

Cited By ~ 72

Author(s):

P. JARNE ◽

A. THÉRON

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Mating System ◽

Natural Populations ◽

Structured Populations ◽

Biological Traits ◽

Migration Rates ◽

External Data ◽

Selective Interference ◽

Host Parasite

Several aspects of the coevolutionary dynamics in host-parasite systems may be better quantified based on analyses of population structure using neutral genetic markers. This includes, for example, the migration rates of hosts and parasites. In this respect, the current situation, especially in fluke-snail systems is unsatisfactory, since basic population genetics data are lacking and the appropriate methodology has rarely been used. After reviewing the forces acting on population structure (e.g. genetic drift or the mating system) and how they can be analysed in models of structured populations, we propose a simplified, indicative framework for conducting analyses of population structure in hosts and parasites. This includes consideration of markers, sampling, data analysis, comparison of structure in hosts and parasites and use of external data (e.g. from population dynamics). We then focus on flukes and snails, highlighting important biological traits with regard to population structure. The few available studies indicate that asexual amplification of flukes within snails strongly influences adult flukes populations. They also show that the genetic structure among populations in strongly affected by traits in other than snails (e.g. definitive host dispersal behaviour), as snails populations have limited migration. Finally more studies would allow us to deepen our current understanding of selective interference between flukes and snails (e.g. manipulation of host mating system by parasites), and evaluate how this affect population structure at neutral markers.

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Landscape genetic structure of natural populations of Acacia caven in Argentina

Tree Genetics & Genomes ◽

10.1007/s11295-012-0479-6 ◽

2012 ◽

Vol 8 (4) ◽

pp. 911-924 ◽

Cited By ~ 9

Author(s):

Carolina L. Pometti ◽

Cecilia F. Bessega ◽

Juan C. Vilardi ◽

Beatriz O. Saidman

Keyword(s):

Genetic Structure ◽

Natural Populations ◽

Acacia Caven ◽

Landscape Genetic

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Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

10.1101/2020.02.29.971309 ◽

2020 ◽

Cited By ~ 2

Author(s):

Ebenezer Foster-Nyarko ◽

Nabil-Fareed Alikhan ◽

Anuradha Ravi ◽

Gaëtan Thilliez ◽

Nicholas Thomson ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Antimicrobial Resistance ◽

Genome Sequencing ◽

Host Species ◽

The Gambia ◽

Genomic Diversity ◽

Whole Genome ◽

E Coli ◽

Sequence Types

AbstractIncreasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity, and antimicrobial resistance in Escherichia coli isolates from four species of non-human primate in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on eleven isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2—characterised by strains that cause human extraintestinal infections—and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and seven alleles respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes—indicating novel diversity specific to the primate niche. Our results are of public health importance, considering the increasing contact between humans and wild non-human primates.Impact statementLittle is known about the population structure, virulence potential and the burden of antimicrobial resistance among Escherichia coli from wild non-human primates, despite increased exposure to humans through the fragmentation of natural habitats. Previous studies, primarily involving captive animals, have highlighted the potential for bacterial exchange between non-human primates and humans living nearby, including strains associated with intestinal pathology. Using multiple-colony sampling and whole-genome sequencing, we investigated the strain distribution and population structure of E. coli from wild non-human primates from the Gambia. Our results indicate that these monkeys harbour strains that can cause extraintestinal infections in humans. We document the transmission of virulent E. coli strains between monkeys of the same species sharing a common habitat and evidence of recent interaction between strains from humans and wild non-human primates. Also, we present complete genome assemblies for five novel sequence types of E. coli.Author notesAll supporting data, code and protocols have been provided within the article or through supplementary data files. Nine supplementary figures and six supplementary files are available with the online version of this article.AbbreviationsExPEC, Extraintestinal pathogenic Escherichia coli; ST, Sequence type; AMR, Antimicrobial resistance; MLST, Multi-locus sequence typing; VFDB, Virulence factors database; SNP, single nucleotide polymorphism; SPRI, Solid phase reversible immobilisation.Data summaryThe raw sequences and polished assemblies from this study are available in the National Center for Biotechnology Information (NCBI) Short Read Archive, under the BioProject accession number PRJNA604701. The full list and characteristics of these strains and other reference strains used in the analyses are presented in Table 1 and Supplementary Files 1-4 (available with the online version of this article).

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PERIODIC SELECTION, INFECTIOUS GENE EXCHANGE AND THE GENETIC STRUCTURE OF E. COLI POPULATIONS

Genetics ◽

10.1093/genetics/99.1.1 ◽

1981 ◽

Vol 99 (1) ◽

pp. 1-23 ◽

Cited By ~ 3

Author(s):

Bruce R Levin

Keyword(s):

Genetic Structure ◽

Genetic Variability ◽

Bacterial Species ◽

A Priori ◽

Natural Populations ◽

Gene Exchange ◽

Effective Population ◽

Bacterial Populations ◽

E Coli ◽

Population Sizes

ABSTRACT As a consequence of sequential replacements by clones of higher fitness (periodic selection), bacterial populations would be continually purged of genetic variability, and the fate of selectively neutral alleles in very large populations of bacteria would be similar to that in demes of sexually reproducing organisms with small genetically effective population sizes. The significance of periodic selection in reducing genetic variability in these clonally reproducing species is dependent on the amount of genetic exchange between clones (recombination). In an effort to determine the relationship between the rates of periodic selection, recombination and the genetically effective sizes of bacterial populations, a model for periodic selection and infectious gene exchange has been developed and its properties analyzed. It shows that, for a given periodic selection regime, genetically effective population size increases exponentially with the rate of recombination.—With the parameters of this model in the range anticipated for natural populations of E. coli, the purging effects of periodic selection on genetic variability are significant; individual populations or lineages of this bacterial species would have very small genetically effective population sizes.—Based on this result, some other a priori considerations and a review of the results of epidemiological and genetic variability studies, it is postulated that E. coli is composed of a relatively limited number of geographically widespread and genetically nearly isolated and monomorphic lineages. The implications of these considerations of the genetic structure of E. coli populations of the interpretation of protein variation and the neutral gene hypothesis are discussed.

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