scholarly journals Evidence for “inter- and intraspecific horizontal genetic transfers” between anciently asexual bdelloid rotifers is explained by cross-contamination

2017 ◽  
Author(s):  
Christopher G. Wilson ◽  
Reuben W. Nowell ◽  
Timothy G. Barraclough
Keyword(s):  
Sequence Homology ◽  
Horizontal Transfer ◽  
Natural Populations ◽  
Cross Contamination ◽  
Genetic Transfer ◽  
Genomic Features ◽  
Bdelloid Rotifers ◽  
Maintenance Of Sex ◽  
Nuclear Loci ◽  
Donor Species

SummaryBdelloid rotifers are microscopic invertebrates thought to have evolved for millions of years without sexual reproduction. They have attracted the attention of biologists puzzled by the maintenance of sex among nearly all other eukaryotes. Bdelloid genomes have an unusually high proportion of horizontally acquired non-metazoan genes. This well-substantiated finding has invited speculation that homologous horizontal transfer between rotifers also may occur, perhaps even 'replacing' sex. A 2016 study in Current Biology claimed to supply evidence for this hypothesis. The authors sampled rotifers of the genus Adineta from natural populations and sequenced one mitochondrial and four nuclear loci. For several samples, species assignments were incongruent among loci, which the authors interpreted as evidence of "interspecific genetic exchanges". Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more divergent mitochondrial and ribosomal sequences, indicating contamination with DNA from additional animals belonging to the supposed “donor species”. We also show that “exchanged” molecules share only 75% sequence homology, a degree of divergence incompatible with established mechanisms of recombination and genomic features of Adineta. These findings are parsimoniously explained by cross-contamination of tubes with animals or DNA from different species. Given the proportion of tubes contaminated in this way, we show by calculation that evidence for "intraspecific horizontal exchange" in the same dataset is explained by contamination with conspecific DNA. On the clear evidence of these analyses, the 2016 study provides no reliable support for the hypothesis of horizontal genetic transfer between or within these bdelloid species.

scholarly journals Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

2020 ◽  
Vol 10 (5) ◽  
pp. 1553-1561 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Network Analysis ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

scholarly journals Establishment and maintenance of aphid endosymbionts after horizontal transfer is dependent on host genotype

2017 ◽  
Vol 13 (5) ◽  
pp. 20170016 ◽  
Author(s):  
Benjamin J. Parker ◽  
Ailsa H. C. McLean ◽  
Jan Hrček ◽  
Nicole M. Gerardo ◽  
H. Charles J. Godfray
Keyword(s):  
Natural Selection ◽  
Microbial Communities ◽  
Host Plant ◽  
Intraspecific Variation ◽  
Horizontal Transfer ◽  
Natural Populations ◽  
Host Genotype ◽  
Pea Aphids

Animal-associated microbial communities have important effects on host phenotypes. Individuals within and among species differ in the strains and species of microbes that they harbour, but how natural selection shapes the distribution and abundance of symbionts in natural populations is not well understood. Symbionts can be beneficial in certain environments but also impose costs on their hosts. Consequently, individuals that can or cannot associate with symbionts will be favoured under different ecological circumstances. As a result, we predict that individuals within a species vary in terms of how well they accept and maintain symbionts. In pea aphids, the frequency of endosymbionts varies among host-plant-associated populations (‘biotypes’). We show that aphid genotypes from different biotypes vary in how well they accept and maintain symbionts after horizontal transfer. We find that aphids from biotypes that frequently harbour symbionts are better able to associate with novel symbionts than those from biotypes that less frequently harbour symbionts. Intraspecific variation in the ability of hosts to interact with symbionts is an understudied factor explaining patterns of host–symbiont association.

The prevalence and evolution of sex in microorganisms

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 775-780 ◽  
Author(s):  
Jianping Xu
Keyword(s):  
Sexual Reproduction ◽  
Recent Progress ◽  
Natural Populations ◽  
Microbial Populations ◽  
Model Organisms ◽  
Costs And Benefits ◽  
Evolution Of Sex ◽  
Excellent Model ◽  
Maintenance Of Sex ◽  
Eukaryotic Microbes

The origin of sex and how sex is maintained are among the biggest puzzles in biology. Most investigations into this problem have focused on complex eukaryotes like animals and plants. This mini-review summarizes recent progress in our understanding of the evolution of sex, highlighting results from studies of experimental and natural populations of microorganisms. Increasing evidence indicates that sexual reproduction in natural populations of viruses, bacteria, and eukaryotic microbes is much more prevalent than previously thought. In addition, investigations using experimental microbial populations are providing important parameters relevant to our understanding of the origin and maintenance of sex. It is argued that microbes are excellent model organisms to explore the mechanisms responsible for the evolution of sex.Key words: costs and benefits of sex, natural populations, experimental populations, Müller's Ratchet, interaction among mutations, loss of sex.

scholarly journals Comparison of the Efficacies of Oral β-Lactams in Selection of Haemophilus influenzae Transformants with Mutated ftsI Genes

2008 ◽  
Vol 52 (5) ◽  
pp. 1880-1883 ◽  
Author(s):  
Sho Takahata ◽  
Yoshihisa Kato ◽  
Yumiko Sanbongi ◽  
Kazunori Maebashi ◽  
Takashi Ida
Keyword(s):  
Haemophilus Influenzae ◽  
Horizontal Transfer ◽  
Susceptible Strain ◽  
Genetic Transfer ◽  
Selection Window ◽  
Selection Of

ABSTRACT Horizontal transfer of the mutated ftsI gene from β-lactamase-nonproducing ampicillin-resistant (BLNAR) Haemophilus influenzae to a susceptible strain was examined in vitro under selection with nine oral β-lactams (ampicillin, amoxicillin, cefprozil, cefuroxime, cefpodoxime, cefdinir, cefcapene, cefditoren, and tebipenem). Compared to the penicillins and the carbapenem, the cephalosporins showed a wide selection window for the genetic transfer.

scholarly journals Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap.

Genetics ◽  
1992 ◽  
Vol 131 (3) ◽  
pp. 753-760 ◽  
Author(s):  
J G Lawrence ◽  
D L Hartl
Keyword(s):  
Horizontal Transfer ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Genetic Material ◽  
Molecular Data ◽  
Data Sets ◽  
Similarity Coefficients ◽  
Genetic Transfer ◽  
Statistical Framework ◽  
Partial Data

Abstract Inconsistencies in taxonomic relationships implicit in different sets of nucleic acid sequences potentially result from horizontal transfer of genetic material between genomes. A nonparametric method is proposed to determine whether such inconsistencies are statistically significant. A similarity coefficient is calculated from ranked pairwise identities and evaluated against a distribution of similarity coefficients generated from resampled data. Subsequent analyses of partial data sets, obtained by the elimination of individual taxa, identify particular taxa to which the significance may be attributed, and can sometimes help in distinguishing horizontal genetic transfer from inconsistencies due to convergent evolution or variation in evolutionary rate. The method was successfully applied to data sets that were not found to be significantly different with existing methods that use comparisons of phylogenetic trees. The new statistical framework is also applicable to the inference of horizontal transfer from restriction fragment length polymorphism distributions and protein sequences.

scholarly journals Evidence for horizontal transmission of the P transposable element between Drosophila species.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 339-355 ◽  
Author(s):  
S B Daniels ◽  
K R Peterson ◽  
L D Strausbaugh ◽  
M G Kidwell ◽  
A Chovnick
Keyword(s):  
Horizontal Transfer ◽  
Horizontal Transmission ◽  
Natural Populations ◽  
P Element ◽  
Base Substitution ◽  
Potential Donor ◽  
Transfer Event ◽  
P Elements ◽  
Autonomous Element ◽  
Group A

Abstract Several studies have suggested that P elements have rapidly spread through natural populations of Drosophila melanogaster within the last four decades. This observation, together with the observation that P elements are absent in the other species of the melanogaster subgroup, has lead to the suggestion that P elements may have entered the D. melanogaster genome by horizontal transmission from some more distantly related species. In an effort to identify the potential donor in the horizontal transfer event, we have undertaken an extensive survey of the genus Drosophila using Southern blot analysis. The results showed that P-homologous sequences are essentially confined to the subgenus Sophophora. The strongest P hybridization occurs in species from the closely related willistoni group. A wild-derived strain of D. willistoni was subsequently selected for a more comprehensive molecular examination. As part of the analysis, a complete P element was cloned and sequenced from this line. Its nucleotide sequence was found to be identical to the D. melanogaster canonical P, with the exception of a single base substitution at position 32. When the cloned element was injected into D. melanogaster embryos, it was able to both promote transposition of a coinjected marked transposon and induce singed-weak mutability, thus demonstrating its ability to function as an autonomous element. The results of this study suggest that D. willistoni may have served as the donor species in the horizontal transfer of P elements to D. melanogaster.

scholarly journals Cross-Contamination Explains “Inter and Intraspecific Horizontal Genetic Transfers” between Asexual Bdelloid Rotifers

2018 ◽  
Vol 28 (15) ◽  
pp. 2436-2444.e14 ◽  
Author(s):  
Christopher G. Wilson ◽  
Reuben W. Nowell ◽  
Timothy G. Barraclough
Keyword(s):  
Cross Contamination ◽  
Bdelloid Rotifers

scholarly journals Patterns of linkage disequilibrium reveal genome architecture in chum salmon

2019 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Linkage Disequilibrium ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions ◽  
Sexually Antagonistic Selection ◽  
Gene Complexes

AbstractMany studies exclude loci exhibiting linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the signal of the sex-determining region was only obvious after restricting genetic analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. The results of this study highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of ignoring or excluding loci exhibiting LD.

scholarly journals Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution

2017 ◽  
Author(s):  
Reuben W. Nowell ◽  
Pedro Almeida ◽  
Christopher G. Wilson ◽  
Thomas P. Smith ◽  
Diego Fontaneto ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Desiccation Tolerance ◽  
Unique Feature ◽  
Genome Sequences ◽  
Genomic Features ◽  
Bdelloid Rotifers ◽  
Freshwater Habitats ◽  
Animal Phyla

AbstractBdelloid rotifers are microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we evaluate the relative effects of asexuality and desiccation tolerance on genome evolution by comparing whole genome sequences for three bdelloid species: Adineta ricciae (desiccation tolerant), Rotaria macrura and Rotaria magnacalcarata (both desiccation intolerant) to the only published bdelloid genome to date, that of Adineta vaga (also desiccation tolerant). We find that tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is low, well within the range observed between alleles in obligately sexual, diploid animals. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. These findings are contrary to current understanding of the role of desiccation in shaping the bdelloid genome, and indicate that various features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred non-metazoan genes encoded in both desiccating and non-desiccating bdelloid species, and show that this is a unique feature of bdelloids among related animal phyla. Comparisons within bdelloids and to other desiccation-tolerant animals, however, again call into question the purported role of desiccation in horizontal transfer.

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