Origin Of Genetic Diversity Research Articles

Meiosis I causes a high spontaneous mutation rate in a multicellular red alga (Pyropia yezoensis) with a complex life cycle

Mutations are the origin of genetic diversity and are fundamental parameters needed to understand the molecular evolution of species. Estimations of mutation rates have been conducted for many diverse taxa, although rates in several major eukaryotic lineages remain unexplored. Here, the first estimation is reported of the spontaneous mutation rate for the multicellular eukaryote red alga, Pyropia yezoensis, which exhibits a complex life cycle. An estimated mutation rate of 2.97 × 10−8 (95 % CI: 2.16 × 10−8–3.99 × 10−8) per site per generation was generated for the primary life cycle, the sexual cycle, which is the highest sexual mutation rate among published sexual plants. Combined with tetrad analysis, meiosis I was identified as the primary period responsible for the high mutation rate during the complex life cycle of P. yezoensis. This result provides direct evidence for the “meiosis is mutagenic” hypothesis for multicellular organisms. The accurate estimate of the mutation rate of P. yezoensis also informs several immediate applications. Based on the above estimate, the effective population size (Ne) of P. yezoensis was estimated at about 19,000, with extensive haploid phases and asexual reproduction through monospores possibly leading to linked selection that may reduce the genome-wide genetic diversity of P. yezoensis and consequently influence Ne estimation. Lastly, P. yezoensis was estimated to have diverged from P. haitanensis about 4.2 Ma, representing a more recent date than estimates from fossil-calibrated phylogenies. These findings provide valuable new information for understanding the evolution of red algae, in addition to the underlying mechanism of mutations.

Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.

Paraguay has been severely affected by emergent Zika and chikungunya viruses, and dengue virus is endemic. To learn more about the origins of genetic diversity and epidemiologic history of these viruses in Paraguay, we deployed portable sequencing technologies to strengthen genomic surveillance and determine the evolutionary and epidemic history of arthropod-borne viruses (arboviruses). Samples stored at the Paraguay National Central Laboratory were sequenced and subjected to phylogenetic analysis. Among 33 virus genomes generated, we identified 2 genotypes of chikungunya and 2 serotypes of dengue virus that circulated in Paraguay during 2014–2018; the main source of these virus lineages was estimated to be Brazil. The evolutionary history inferred by our analyses precisely matched the available travel history of the patients. The genomic surveillance approach used was valuable for describing the epidemiologic history of arboviruses and can be used to determine the origins and evolution of future arbovirus outbreaks.

First Estimation of the Spontaneous Mutation Rate in Diatoms.

Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.

An Ancient Integration in a Plant NLR is Maintained as a Trans-species Polymorphism

The origin of genetic diversity in a species is a product of novel mutation and alleles maintained during speciation. Identification of alleles that are derived from a common ancestor is critical for understanding the selective processes experienced during speciation events. Here, we report on the inter- and intra-specific diversity of plant immune receptors in the Mla locus across Poaceae species. These immune receptors belong to the class of cytoplasmic-nuclear localized nucleotide-binding leucine-rich repeat (NLR) proteins. Plant immune receptors are under constant selective pressure to maintain resistance to plant pathogens, and novel mutations leading to improved immune responses are selected. We discovered a fusion of the plant immune receptor RGH2 with a component of the exocyst complex (Exo70). Phylogenetic analysis of Exo70 gene families from Poaceae species found that the integrated Exo70 was derived from Exo70F1. To identify the origin of this gene fusion, we assembled leaf transcriptomes from diverse Poaceae species. Inter-specific conservation in the RGH2- Exo70F1 gene fusion was found in several Pooideae species, whereas Brachypodium distachyon RGH2 is fused to a receptor-like kinase. To establish the time of gene fusion, we performed phylogenetic analysis using non-integrated and integrated Exo70F1. We found a diphyletic tree composed of non-integrated Exo70F1 and integrated Exo70F1, with Exo70F1 from B. distachyon and B. stacei forming an outgroup. This indicates that a single gene fusion event occurred after the speciation of Brachypodieae, but prior to Poeae-Triticeae radiation. These results, coupled with the observation of inter- and intra-specific variation in RGH2, demonstrate the maintenance of RGH2-Exo70F1 as a trans-species polymorphism over 24 My.

Alpine Crossroads or Origin of Genetic Diversity? Comparative Phylogeography of Two Sympatric Microgastropod Species

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa – Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) – by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant ‘hot-spot’ for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.

Xenogamy and Current Obesity Pandemics

This article unites the results from an integrative reconsideration of actual data about obesity from the viewpoint of recent developments in general pathology, epidemiology, immunology, genetics, and evolution. The focus is on the origin of genetic diversity in obesity manifestations on different levels of the disease. In contrast to the current paradigm of nutritive origin of obesity, the revealed set of evidences shows that the origin of obesity is based on either hereditary or post-infectious incongruence between the regulators of fat metabolism and their receptors. The incongruence may be created either by the destruction of receptors during infection or by genome mutations, which by natural selection, lead both to life-saving incongruence between the infectious agent and its receptor, and simultaneously, in evolution to a life-threatening obesogenic incongruence in the regulator-receptor interaction. The pandemic spread of obesity is induced by xenogamous intercourse between constitutionally incongruent ethnoses, which regulator-receptor evolution has processed at different epidemic conditions. The achieved results have allowed a replenish model for the molecular pathogenesis of obesity to explain the genetics of both obesity and its pandemic spread. The formerly maladroit issues of obesity origin, genetic, pathogenesis, and pandemic spread are transformed in an entire replenished system.

Medical Genetic Polymorphisms as Markers of Evolutionary Forces Within the Human Genome: Hypotheses Focusing on Natural Selection in the Basque Population

Natural selection, drift, and gene flow are the three major evolutionary forces at the origin of genetic diversity among human populations. To further explore these mechanisms, we present an innovative approach using various medical genetic markers and focusing on the Basque population. From this study we can confirm the important role of drift in this endogamous human group and can report some disorders related to founder effects. Most important, the peculiar distribution of various polymorphisms, such as blood group O, factor V Leiden, DF508, C282Y, and CCR5 D32 mutations, which are implicated in resistance to infection, hemostasis, or iron conservation, could be interpreted as an adaptive profile. Multidisciplinary data have shown that the Neolithic period arrived significantly later in this southwestern corner of Europe. We hypothesize that the long-lasting Paleolithic mode of life, especially regarding nutrition and microbial exposure, was at the origin of this selective pressure within this population of ancient local ancestry. This approach could open new avenues in the field of population genetics.

Medical Genetic Polymorphisms as Markers of Evolutionary Forces Within the Human Genome: Hypotheses Focusing on Natural Selection in the Basque Population

Natural selection, drift, and gene flow are the three major evolutionary forces at the origin of genetic diversity among human populations. To further explore these mechanisms, we present an innovative approach using various medical genetic markers and focusing on the Basque population. From this study we can confirm the important role of drift in this endogamous human group and can report some disorders related to founder effects. Most important, the peculiar distribution of various polymorphisms, such as blood group O, factor V Leiden, DF508, C282Y, and CCR5 D32 mutations, which are implicated in resistance to infection, hemostasis, or iron conservation, could be interpreted as an adaptive profile. Multidisciplinary data have shown that the Neolithic period arrived significantly later in this southwestern corner of Europe. We hypothesize that the long-lasting Paleolithic mode of life, especially regarding nutrition and microbial exposure, was at the origin of this selective pressure within this population of ancient local ancestry. This approach could open new avenues in the field of population genetics.

Genetic diversity of Potamogeton anguillanus in Lake Biwa, Japan

The genetic structure of Potamogeton anguillanus in Lake Biwa, Japan was surveyed by enzyme electrophoresis. Polymorphic banding patterns were observed in four of eight enzymes investigated. Based on the combination of the single enzyme phenotypes, 27 multi-enzyme phenotypes (MEPs) were determined in the whole lake based on 258 shoot samples collected from 14 local populations. Most of the local populations were polymorphic and involved one to eight unique MEPs. A mapping survey of MEPs in selected quadrats showed establishment of ramets with different genotypes and the clonal spread of the species. The origin of genetic diversity in the species may partly be due to recurrent hybridization. Sexual reproduction may also be involved.

On the Origin of Genetic Diversity

The organic diversity found in nature today is ultimately a consequence of a continuous cycle of building up genetic diversity, which is subsequently channeled by natural selection, chance events, and by geographic or other modes of speciation. Whereas modern evolutionary theory provides detailed explanations of the mechanisms channeling genetic diversity, little is known on the evolutionary forces responsible for the presence and the properties of processes that create genetic diversity. Conventionally, genetic diversity is viewed as the outcome of mutation mechanisms that are not themselves optimized by natural selection. In contrast, a great number of hypotheses are available on the adaptive significance of meiosis, sex and general genetic recombination in eukaryotes, which are mechanisms for the “management” of genetic diversity, but not for its production. In this contribution, we argue that bacteria have evolved elaborate mechanisms for the production of genetic diversity. These mechanisms could themselves be subject to adaptation by natural selection. A selection mechanism termed second-order selection is discussed which could account for the abundance of genes that cause random DNA sequence variation in bacteria.