Predominant Evolutionary Force Research Articles

Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut

Probiotics often acquire potentially adaptive mutations in vivo, gaining new functional traits through gut selection. While both the host and microbiome can contribute to probiotics’ genetic evolution, separating the microbiome and the host’s contribution to such selective pressures remains challenging. Here, we introduced germ-free (GF) and specific pathogen-free (SPF) mouse models to track how probiotic strains, i.e., Lactiplantibacillus plantarum HNU082 (Lp082) and Bifidobacterium animalis subsp. lactis V9 (BV9), genetically evolved under selection pressures derived from host factors alone and both host and microbial ecological factors. Notably, compared to the genome of a probiotic strain before consumption, the host only elicited <15 probiotic mutations in probiotic genomes that emerged in the luminal environment of GF mice, while a total of 840 mutations in Lp082 mutants and 21,579 mutations in BV9 were found in SPF mice, <0.25% of those derived from both factors that were never captured by other experimental evolution studies, indicating that keen microbial competitions exhibited the predominant evolutionary force in shaping probiotic genetic composition (>99.75%). For a given probiotic, functional genes occurring in potentially adaptive mutations induced by hosts (GF mice) were all shared with those found in mutants of SPF mice. Collectively, the native microbiome consistently drove a more rapid and divergent genetic evolution of probiotic strains in seven days of colonization than host factors did. Our study further laid a theoretical foundation for genetically engineering probiotics for better gut adaptation through in vitro artificial gut ecosystems without the selection pressures derived from host factors.

Natural selection drives the evolution of mitogenomes in Acrossocheilus

The mitochondrial genome plays a crucial role in the balance of energy and heat production in organisms and, thus, may be under natural selection due to its potential role in adaptive divergence and speciation. Here, we studied natural selection on the mitogenome of Acrossocheilus (Cypriniformes: Cyprinidae), a genus of fish that inhabits a broad latitudinal distribution ranging from the tropics and subtropics through temperate regions. Specifically, we used 25 published mitogenome sequences of Acrossocheilus species to investigate phylogenetic relationships in this genus and detected signals of positive selection on 13 protein-coding, mitochondrial genes. We found that relaxed purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, we also found evidence of diversifying selection on some codons, indicating episodes of positive selection. Additionally, we analyzed the mitogenomic data within an environmental modeling framework and found that the Ka/Ks ratio of ATP6 may correlated with a mean diurnal temperature range (p = 0.0449), while the Ka/Ks ratio of COX2 may correlated with precipitation during the driest month (p = 0.00761). These results suggest that the mitogenomes of Acrossocheilus species may be involved in evolutionary adaptations to different habitats. Based on this, we believe that our study provides a new insight into the role of the mitochondrial genome of Acrossocheilus species in adaptation to different environments. During our study, we also discovered several cases of paraphyly and polyphyly among accessions of species and their putative synonyms. Thus, our study suggests that a careful reassessment of the taxonomy of Acrossocheilus is using high-quality molecular data merited.

Natural selection drives population divergence for local adaptation in a wheat pathogen

Evolution favors the emergence of locally-adapted optimum phenotypes that are likely to differ across a wide array of environmental conditions. The emergence of favorable adaptive characteristics is accelerated in agricultural pathogens due to the unique properties of agro-ecosystems. We performed a QST - FST comparison using 164 strains of Parastagonospora nodorum sampled from eight global field populations to disentangle the predominant evolutionary forces driving population divergence in a wheat pathogen. We used digital image analysis to obtain quantitative measurements of growth rate and melanization at different temperatures and under different fungicide concentrations in a common garden experiment. FST measures were based on complete genome sequences obtained for all 164 isolates. Our analyses indicated that all measured traits were under selection. Growth rates at 18 °C and 24 °C were under stabilizing selection (QST < FST), while diversifying selection (QST > FST) was the predominant evolutionary force affecting growth under fungicide and high temperature stress. Stabilizing selection (QST < FST) was the predominant force affecting melanization across the different environments. Melanin production increased at 30 °C but was negatively correlated with higher growth rates, consistent with a trade-off under heat stress. Our results demonstrate that global populations of P. nodorum possess significant evolutionary potential to adapt to changing local conditions, including warmer temperatures and applications of fungicides.

Contrasting evolutionary processes drive morphological and genetic differentiation in a subtropical fir (Abies, Pinaceae) species complex

AbstractInteracting stochastic and selective forces drive population and species divergence. Such interaction may generate contrasting clines between genetic and phenotypic factors, which can be related to either geographical or environmental variation depending on the predominant evolutionary force (which in its turn is partly determined by population size). Here, we investigated whether the morphological and genetic differentiation across a species complex in Abies in central Mexico fits isolation by distance (IBD) or isolation-by-adaptation (IBA) frameworks. This complex includes two species (A. religiosa and A. flinckii) with discernible morphological and environmental differences and dissimilar range sizes. After comparing variation at nuclear SSR loci and diagnostic morphological traits of needles with the climate variables contributing to ecological differentiation, we found that the widely distributed A. religiosa has more genetic diversity and is morphologically more heterogeneous than the geographically restricted A. flinckii. Morphological differentiation at three physiologically important traits (needle thickness, number of stomata rows and location of the resin duct) is significantly correlated with geography in A. flinckii (indicative of IBD), but is significantly associated with climate variation in A. religiosa (suggesting IBA). In agreement with quantitative genetics theory, PST (phenotypic differentiation)-G’ST (genetic differentiation) comparisons indicate contrasting contributions of putatively adaptive (A. religiosa) and stochastic (A. flinckii) factors to the morphological differentiation of species related to their population size. The integration of such quantitative genetic/evolutionary aspects may reinforce species descriptions and help in disentangling resilient taxonomic discordance.

Molecular Evolutionary Analysis of the HCRTR Gene Family in Vertebrates.

Hypocretin system is composed of hypocretins (hcrts) and their receptors (hcrtrs), which has multiple vital functions. Hypocretins work via hypocretin receptors and it is reported that functional differentiation occurred in hcrtrs. It is necessary to figure out the evolution process of hypocretin receptors. In our study, we adopt a comprehensive approach and various bioinformatics tools to analyse the evolution process of HCRTR gene family. It turns out that the second round of whole genome duplication in early vertebrate ancestry and the independent round in fish ancestry may contribute to the diversity of HCRTR gene family. HCRTR1 of fishes and mammals are not the same receptor, which means that there are three members in the family. HCRTR2 is proved to be the most ancient one in HCRTR gene family. After duplication events, the structure of HCRTR1 diverged from HCRTR2 owing to relaxed selective pressure. Negative selection is the predominant evolutionary force acting on the HCRTR gene family but HCRTR1 of mammals is found to be subjected to positive selection. Our study gains insight into the molecular evolution process of HCRTR gene family, which contributes to the further study of the system.

Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot.

Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.

Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus

Considering the homogeneity of marine environment, temperature might be a main environmental factor responsible for local adaptation across a wide latitudinal range. We reconstructed population structure and performed selection tests on a fragment of 1821 bp of the mitochondrial ATPase 6 (ATP6) and cytochrome b (CYTB) genes of Sebastiscus marmoratus sampled from five populations throughout the northwest Pacific Ocean across a large latitudinal range. In line with the results of F st statistics, significant population structure was detected by applying PCoA and STRUCTURE analysis, which showed discrepant genetic patterns compared to previous studies using neutral markers. Selection tests showed that purifying selection was the predominant evolutionary force acting on the analyzed sequences. Valine substitution by Alanine in a single codon 372 in CYTB gene was detected predominantly (93%) in FA population and temperature was a potentially relevant environmental feature. These findings suggest that local adaptation might be shaping the population structure of marbled rockfish. Further, discrepant patterns of population structure suggested that discerning contributions of different mechanisms in shaping and maintaining patterns of population structure is essential to better understand complex population structure and dynamics of marine organisms.

The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae)

The genus Rattus is one of the main pest genus of rodent. Most species of the genus carry all kinds of pathogenic bacteria to human being. They are traditionally considered to be a least understood group. The complete mitochondrial genome of the White-Footed Indochinese Rat, Rattus nitidus was determined in this study. The characterization of mitochondrial genomes of Rattus genus was also analyzed based on comprehensive comparison. The result of evolutionary patterns of protein-coding genes (PCGs) suggested purifying selection was the predominant evolutionary forces in the mitochondrial genomes of Rattus genus. The NADH dehydrogenase 4 gene (ND4) showed a highly elevated Ka/Ks ratio compared to the other protein-coding genes, which indicated ND4 was most likely under relaxed selection pressure. Phylogenetic analysis provided a well-supported outline of Rattus genus, and revealed two groups in the genus. R. nitidus had a sister relationship with R. norvegicus.

Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias).

The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species' divergence.

Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.

Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

BackgroundHantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments.MethodsA total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments.ResultsAll three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution.ConclusionsThere is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

Molecular evolution and functional divergence of X-intrinsic protein genes in plants.

X-intrinsic proteins (XIPs) are a novel class of major intrinsic proteins found in diverse organisms. Recently, XIP genes have been reported to be involved in the transport of a wide range of hydrophobic solutes; however, the evolutionary forces driving their structural and functional divergence in plants are poorly understood. In the present study, comprehensive bioinformatics analyses were performed to gain insight into the molecular and evolutionary mechanisms driving this structural and functional diversification. Phylogenetic analyses have revealed the major lineage-specific expansions of XIP genes in plants. Within the eudicots, XIP genes have diverged into Asterid and Rosid-specific phylogenetic lineages and have also undergone several independent duplications during the course of evolution. Investigation of functional divergence at the protein level showed evidence for shifting evolutionary rate and/or altered constraints on the physiochemical properties of specific amino acid sites following gene duplication. Selection pressure analyses suggest that purifying selection is the predominant evolutionary force acting on the XIP gene subfamily, along with episodic positive selection. However, only a few amino acid sites were found to be subjected to such episodic positive selection. Furthermore, protein functional divergence analysis has identified critical amino acid residues, which must be validated by future experimental studies, that could provide new insights into the role of XIPs in transport of a wide range solutes of physiological importance.

Genetic analysis suggests high conservation value of peripheral populations of Chihuahau chub (Gila nigrescens)

Genetic drift is expected to be the predominant evolutionary force in small, fragmented peripheral populations, which can lead to divergent allele frequencies and lowered diversity compared to the core population. Peripheral populations are not considered a high priority for conservation for this reason. However, peripheral populations may possess unique genetic variability not found elsewhere in the species’ range, and may be especially important if core populations are at extirpation risk. Here, we characterized levels and patterns of genetic diversity at microsatellites and mtDNA for the peripheral populations of Chihuahua chub in New Mexico, and compared these results to populations in Mexico including a new locality in the Rio Yaqui basin. All populations of Chihuahua chub in New Mexico were genetically depauperate as expected due to their small and peripheral status, and harbored distinct variation compared to those in Mexico. Allele and haplotype frequencies were divergent between New Mexican and Mexican populations, and mitochondrial haplotypes were not shared between them. All New Mexican populations were significantly divergent from one another suggesting little genetic exchange. New Mexican populations also exhibited relatively small genetic effective size. Chihuahua chub in New Mexico thus represent a unique component of the species’ evolutionary legacy and hence suggests high conservation value of this peripheral population. Conservation value of this population is bolstered by the fact that Chihuahua chub has more legal protection than counterparts in Mexico.

Why does the immune system of Atlantic cod lack MHC II?

MHC II, a major feature of the adaptive immune system, is lacking in Atlantic cod, and there are different scenarios (metabolic cost hypothesis or functional shift hypothesis) that might explain this loss. The lack of MHC II coincides with an increased number of genes for MHC I and Toll-like receptors (TLRs).

Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia

Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. In this study, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of Tomato spotted wilt virus (TSWV) from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of 1 or 2 predominant haplotypes and >100 haplotypes represented by a single isolate. No specific haplotypes were associated with geographic area, peanut cultivar, or year of isolation. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for positive selection on single amino acids in each gene on a background of predominant purifying selection acting upon each locus. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Estimates of the population mutation rate suggest that mutation has had a significant effect on the shaping of this population and, together with purifying selection, these forces have been the predominant evolutionary forces influencing the TSWV population in peanut in North Carolina and Virginia.

Strong purifying selection in the silicon transporters of marine and freshwater diatoms

Marine and freshwater diatoms show several important differences in silicon physiology. In addition to containing an order of magnitude more silica in their cell walls, freshwater diatoms also appear to have a less efficient silicic acid uptake mechanism. A novel set of silicon transporters (SITs), encoded by a small gene family, import silicic acid from the environment into the diatom cell. Some evidence suggests that the disparity in uptake efficiency between marine and freshwater diatoms might be attributable to different demands on SITs in the two environments. To test this hypothesis, partial SIT genes were cloned and sequenced from 45 species of Thalassiosirales, a diatom lineage with high diversity in marine and freshwaters. Phylogenetically based codon substitution models were used to test whether SITs from marine and freshwater taxa were under similar selective constraints and whether codons in different structural locations of the protein were under similar functional constraints. Purifying selection is the predominant evolutionary force acting on SITs, irrespective of location in the protein, and differences in efficiency of silicic acid uptake between marine and freshwater diatoms are not due to sequence differences in SITs.

Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host

BackgroundThe ability of emerging pathogens to infect new species is likely related to the diversity of pathogen variants present in existing reservoirs and their degree of genomic plasticity, which determines their ability to adapt to new environments. Certain simian immunodeficiency viruses (SIVcpz, SIVsm) have demonstrated tremendous success in infecting new species, including humans, resulting in the HIV-1 and HIV-2 epidemics. Although SIV diversification has been studied on a population level, the essential substrates for cross-species transmission, namely SIV sequence diversity and the types and extent of viral diversification present in individual reservoir animals have not been elucidated. To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time.ResultsSIVsm demonstrated extensive intra-animal V1V2 length variation and amino acid diversity (le38%), and continual variation in V1V2 N-linked glycosylation consensus sequence frequency and location. Positive selection was the predominant evolutionary force. Temporal sequence shifts suggested continual selection, likely due to evolving antibody responses. In contrast, gag p27 was predominantly under purifying selection. SIVsm V1V2 sequence diversification is at least as great as that in HIV-1 infected humans, indicating that extensive viral diversification in and of itself does not inevitably lead to AIDS.ConclusionPositive diversifying selection in this natural reservoir host is the engine that has driven the evolution of the uniquely adaptable SIV/HIV envelope protein. These studies emphasize the importance of retroviral diversification within individual host reservoir animals as a critical substrate in facilitating cross-species transmission.

Genetic variation at MHC, mitochondrial and microsatellite loci in isolated populations of Brown trout (Salmo trutta)

We have studied levels and distribution of genetic variation in nine isolated populations of Brown trout in NW Spain. In the present study, we have tried to test the importance of preservation of genetic variability for the survival of a set of isolated Brown trout (Salmo trutta) populations from the same river drainage. We screened genetic variation in three different markers, mitochondrial, microsatellites and Major Histocompatibility Complex (MHC), presumed to be under different selective pressures. Overall, genetic diversity varied considerably across populations and the distribution of genetic variation was similar at MHC and microsatellites; highly polymorphic populations at the microsatellite loci were also highly polymorphic at the MHC. We also observed high levels of differentiation among populations. Although we found evidence suggesting that balancing selection has influenced the long term evolution of the MHC, genetic drift seems to have eroded the effect of selection, becoming the predominant evolutionary force shaping genetic variation in some of the smaller populations. Despite current lack of variation at the MHC, these small populations seem to have remained viable for a long time.

Evidence of natural selection for disease resistance in Composite Cross Five (CCV) of barley.

Cambridge Composite Cross Five (CCV) of barley was studied utilising hordeins, restriction fragment length polymorphisms (RFLPs) and reaction to powdery mildew with a view to understanding the genetic changes occurring in the population. Changes in the frequency of individual hordein patterns as well as pattern combinations showed directional trends in successive generations in three parallel populations maintained as discrete populations since 1977 in Cambridge. Certain hordein pattern combinations were more common in the resistance classes and there was a strong association between hordein patterns and mildew reaction. RFLP analysis revealed that 80% of a random sample taken from generation F24 of Population I had the same restriction pattern as that of the cultivar Algerian, which was one of the original 30 parental lines of CCV. This cultivar is the source of the Mla1 allele in barley improvement programmes in Europe. We argue, based on supporting evidence from hordein analysis and tests of reaction to selected mildew isolates of known virulence isolates together with UK virulence surveys, that selection for Mla1 in Cambridge has been the predominant evolutionary force in CCV in Cambridge.

Cytonuclear genetic structure of a hybrid zone in lizards of theSceloporus grammicuscomplex (Sauria, Phrynosomatidae)

Lizards of the Sceloporus grammicus complex are comprised of multiple chromosome races that form several zones of parapatric hybridization in central Mexico. We scored diagnostic mitochondrial DNA (mtDNA) haplotypes and autosomal chromosome markers in a sample of 342 lizards from one well-defined zone between 2n = 34 and 2n = 46 races. A two-part analysis was performed on this data set in an attempt to infer the predominant evolutionary forces shaping the cytonuclear structure of this zone. The complications posed by its spatial structure were addressed by analysing a hierarchical series of smaller subsamples chosen to approximate single mating units. Two critical conclusions were drawn from this first-stage analysis. First and foremost, the three chromosomes have largely concordant cytonuclear disequilibrium patterns within each subsample with adequate numbers of individuals for detecting nonrandom cytonuclear associations. This suggests that the cytonuclear structure of this zone is predominantly a result of deterministic genome-wide forces rather than genetic drift of deterministic forces specific to individual chromosomes or loci. Second, the fit of a series of migration models to the data shows that the cytonuclear structure of the subsamples is well accounted for by continued gene flow from the two parental races alone, with random mating with respect to cytonuclear genotype and no other evolutionary forces. These results motivate several further empirical and theoretical investigations to refine our understanding of the relative roles of migration and other potentially important forces such as natural selection and genetic drift, in this and other hybrid zones.