Parthenogenesis

2020 ◽  
pp. 242-274
Author(s):  
David J. Innes ◽  
France Dufresne
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Dominant Mode ◽  
Ecological Genetics ◽  
Sexual Species ◽  
Genomic Signatures ◽  
Multiple Origins ◽  
Geographic Parthenogenesis ◽  
Sexual And Asexual Reproduction ◽  
Genomic Tools

The dominant mode of reproduction in eucaryotes is sexual. This has been described as a paradox given that sex is much more costly than reproducing asexually, such as by parthenogenesis. In the Crustacea, parthenogenesis is commonly found in the Ostracoda and Branchiopoda (Artemia and Cladocera), and studies of these species have made important contributions to understanding the ecological and evolutionary relationship between sexual and asexual reproduction. With respect to parthenogenesis, researchers have explored its taxonomic distribution and phylogeny, origin and mode, ecological genetics, and genomic signatures. Parthenogenetic Crustacea include both diploid and polyploid clones that have originated multiple times from related sexual species but appear to have a relatively limited evolutionary lifespan. Darwinulid ostracods may be one exception, with no known sexual forms and possibly an example of ancient asexuality, although this is controversial. Most parthenogenetic crustacean groups appear to have a wider geographic distribution than related sexual species and are often found in marginal habitats associated with higher latitudes and altitudes. Such patterns of geographic parthenogenesis have yet to be fully explained, but could possibly be due to colonization and adaptation advantages of asexuality; further studies are required to eliminate polyploidy alone as an explanation. There are many examples of parthenogenetic ostracods, cladocerans, and Artemia showing high levels of genetic diversity likely due to recent multiple origins from related sexual species. Phylogenetic analyses support this explanation and for Artemia and Daphnia, cases have been documented for rare functional males produced by parthenogenetic females that can mate with sexual females as a mechanism for generating new clonal lineages. The diversity of asexual species, combined with prior ecological and genetic information, suggests that crustaceans will continue as important models for understanding parthenogenesis, particularly with the application of new genomic tools.

scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

scholarly journals Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Jian-Qiu Li ◽  
Li Li ◽  
Bao-Quan Fu ◽  
Hong-Bin Yan ◽  
Wan-Zhong Jia
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Sister Group ◽  
Trna Genes ◽  
Mammal Species ◽  
Qinghai Province ◽  
Loop Region ◽  
Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

scholarly journals Population Genetic Structure of Tapesia acuformis in Washington State

2003 ◽  
Vol 93 (6) ◽  
pp. 650-656 ◽  
Author(s):  
G. W. Douhan ◽  
T. D. Murray ◽  
P. S. Dyer
Keyword(s):  
Genetic Structure ◽  
Mating Type ◽  
Asexual Reproduction ◽  
Permutation Test ◽  
Phylogenetic Analyses ◽  
Random Mating ◽  
Likelihood Ratio Statistic ◽  
Washington State ◽  
Homogeneous Population ◽  
Sexual And Asexual Reproduction

Eyespot of wheat is caused by Tapesia yallundae and T. acuformis. Historically, T. yallundae has been considered the more important causal agent of the disease in Washington state and consists of a large homogeneous population with a genetic structure consistent with both sexual and asexual reproduction. T. acuformis has increased significantly in Washington in the past 10 years and apothecia were found recently under natural field conditions, indicating that T. acuformis may have a more important role in eyespot of wheat than previously was thought. To determine the genetic structure of T. acuformis in Washington, 141 single conidial isolates were sampled from four subpopulations in the eastern wheat-growing region of the state. Isolates were scored for mating type and six amplified fragment length polymorphism markers. All markers segregated in a 1:1 ratio and were determined to be unlinked based on genetic analysis of 24 progeny from an in vitro cross. No significant differences in allele frequencies (0.127 < P < 0.809) were found among individual loci across the four subpopulations and over all loci based on contingency table analysis of the log-likelihood ratio statistic G2. Likewise, no overall differences between subpopulations were detected using the population differentiation statistic θ (θ = -0.004, P = 0.537). Random mating could not be rejected within each subpopulation or for the combined data using clone-corrected data sets based on (i) 1:1 ratio of mating-type, (ii) multilocus gametic disequilibrium analyses (index of association), (iii) phylogenetic analyses (parsimony tree length permutation test), and (iv) genotypic diversity analyses. T. acuformis has a genetic structure similar to that of sympatric populations of T. yallundae in Washington, with both sexual and asexual reproduction contributing to the structuring of this species.

scholarly journals Aggregation, defence and warning signals: the evolutionary relationship

2006 ◽  
Vol 273 (1600) ◽  
pp. 2417-2424 ◽  
Author(s):  
Graeme D Ruxton ◽  
Thomas N Sherratt
Keyword(s):  
Prey Species ◽  
Phylogenetic Analyses ◽  
Experimental Studies ◽  
Evolutionary Relationship ◽  
Group Living ◽  
Relative Timing ◽  
Warning Signals ◽  
Definitive Answer ◽  
Relative Rarity ◽  
Alternative Routes

In a seminal contribution, Fisher argued how distastefulness could incrementally evolve in a prey species that was distributed in family groups. Many defended prey species occur in aggregations, but did aggregation facilitate the evolution of defence as Fisher proposed or did the possession of a defence allow individuals to enjoy the benefits of group living? Contemporary theory suggests that it can work both ways: pre-existing defences can make the evolution of gregariousness easier, but gregariousness can also aid the evolution of defence and warning signals. Unfortunately, the key phylogenetic analyses to elucidate the ordering of events have been hampered by the relative rarity of gregarious species, which in itself indicates that aggregation is not a pre-requisite for defence. Like the underlying theory, experimental studies have not given a definitive answer to the relative timing of the evolution of defence and aggregation, except to demonstrate that both orderings are possible. Conspicuous signals are unlikely to have evolved in the absence of a defence and aggregated undefended prey are likely to be vulnerable to predation in the absence of satiation effects. It therefore seems most likely that defence generally preceded the evolution of both aggregation and signalling, but alternative routes may well be possible.

scholarly journals Streptococcal taxonomy based on genome sequence analyses

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 67 ◽  
Author(s):  
Cristiane C Thompson ◽  
Vanessa E Emmel ◽  
Erica L Fonseca ◽  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Amino Acid Identity ◽  
Species Level ◽  
Viridans Streptococci ◽  
Genome Sequences ◽  
Sequence Analyses ◽  
Acid Identity ◽  
Genomic Signatures ◽  
Genomic Tools ◽  
Average Amino Acid Identity ◽  
Genomic Analyses

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance,S. pneumoniae,S. mitis, andS. oralis. AStreptococcusspecies can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

scholarly journals Key Role of Mitochondrial Mutation Leu107Ser (COX1) in Deltamethrin Resistance in Salmon Lice (Lepeophtheirus Salmonis)

2021 ◽  
Author(s):  
Claudia Tschesche ◽  
Michaël Bekaert ◽  
David I. Bassett ◽  
Sally Boyd ◽  
James E. Bron ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Lepeophtheirus Salmonis ◽  
Nucleotide Polymorphisms ◽  
Mitochondrial Mutation ◽  
Mtdna Mutations ◽  
Salmon Lice ◽  
Multiple Origins ◽  
Deltamethrin Resistance

Abstract Deltamethrin (DTM) is used to treat Atlantic salmon (Salmon salar) against salmon lice (Lepeophtheirus salmonis) infestations. However, development of DTM resistance has been reported from North Atlantic L. salmonis populations, in which resistance is associated with mitochondrial (mtDNA) mutations. This study investigated the relationship between DTM resistance and mtDNA single nucleotide polymorphisms (SNPs). A total of 188 L. salmonis collected from Scottish aquaculture sites were assessed using DTM bioassays and genotyped at 18 SNP loci. Genotyping further included archived parasites of known DTM susceptibility status. The results identified eleven mtDNA haplotypes, three of which were associated with DTM resistance. Phylogenetic analyses of haplotypes suggested multiple origins of DTM resistance. L. salmonis laboratory strains IoA-00 and IoA-10 showed similarly high levels (~100-fold) of DTM resistance in bioassays. Both strains differed strongly in mtDNA haplotype, but shared the missense mutation Leu107Ser in the mitochondrial gene cytochrome c oxidase subunit 1 (COX1), which was detected in all further DTM resistant L. salmonis isolates assessed. In crossing experiments with a DTM-susceptible strains, maternal inheritance of DTM resistance is apparent with both IoA-10 (this study) and IoA-02 (earlier reports). We conclude that Leu107Ser (COX1) is a main genetic determinant of DTM resistance in L. salmonis.

scholarly journals Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

2022 ◽  
Vol 9 ◽  
Author(s):  
Jordan R Brock ◽  
Terezie Mandáková ◽  
Michael McKain ◽  
Martin A Lysak ◽  
Kenneth M Olsen
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Diploid Species ◽  
Time Estimation ◽  
Polyploid Species ◽  
Chromosome Counts ◽  
Diploid Parent ◽  
Divergence Time Estimation ◽  
Multiple Origins ◽  
Chloroplast Genomes

Abstract The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

scholarly journals Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens

2017 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele
Keyword(s):  
Host Range ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Dominant Mode ◽  
Diversification Rate ◽  
Broad Host Range ◽  
Diversification Rates ◽  
Host Jump ◽  
Duplication Events ◽  
Range Variation

AbstractThe range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.

scholarly journals Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kadriye Kahraman ◽  
Stuart James Lucas
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Single Copy ◽  
Corylus Avellana ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Complete Chloroplast Genome ◽  
A Genome ◽  
Cp Genome

Abstract Background Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar ‘Tombul’ with multiple annotation tools. Results Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. Conclusion In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

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