Amount Of Sequence Divergence Research Articles

TreeToReads - a pipeline for simulating raw reads from phylogenies

BackgroundUsing phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA’s SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered.ResultsTo resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree.ConclusionsSuch critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering.

Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.

A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co‐evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide‐binding and pathogen‐recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non‐peptide‐binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non‐exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.

A Bayesian Model Comparison Approach to Inferring Positive Selection

A popular approach to detecting positive selection is to estimate the parameters of a probabilistic model of codon evolution and perform inference based on its maximum likelihood parameter values. This approach has been evaluated intensively in a number of simulation studies and found to be robust when the available data set is large. However, uncertainties in the estimated parameter values can lead to errors in the inference, especially when the data set is small or there is insufficient divergence between the sequences. We introduce a Bayesian model comparison approach to infer whether the sequence as a whole contains sites at which the rate of nonsynonymous substitution is greater than the rate of synonymous substitution. We incorporated this probabilistic model comparison into a Bayesian approach to site-specific inference of positive selection. Using simulated sequences, we compared this approach to the commonly used empirical Bayes approach and investigated the effect of tree length on the performance of both methods. We found that the Bayesian approach outperforms the empirical Bayes method when the amount of sequence divergence is small and is less prone to false-positive inference when the sequences are saturated, while the results are indistinguishable for intermediate levels of sequence divergence.

PHYLOGENETIC ANALYSIS ON GENERA OF CORALLOBOTHRIINAE (CESTODA: PROTEOCEPHALIDEA) FROM NORTH AMERICAN ICTALURID FISHES, USING PARTIAL SEQUENCES OF THE 28S RIBOSOMAL GENE

Partial sequences of the 28S rDNA (ribosomal gene) were obtained from a total of 11 populations of 5 species (in 3 genera) of North American corallobothriine proteocephalideans. These included Corallobothrium fimbriatum (3 populations), Corallobothrium parafimbriatum (1 population), Corallotaenia minutia (1 population), Megathylacoides giganteum (2 populations), and Megathylacoides lamothei (4 populations). These sequences were used in a phylogenetic analysis to test the monophyly of Corallobothriinae and to investigate the interrelationships of the North American species. The results indicate that Corallobothriinae, as conventionally understood, is not monophyletic and that only the North American corallobothriines, parasites of ictalurid catfishes, form a monophyletic group. Corallobothrium parafimbriatum is sister taxon to a clade that includes Corallotaenia intermedia and C. minutia and not to its congener C. fimbriatum. Also, M. giganteum from Mexico appears to be more closely related to M. lamothei than to its conspecific in Canada. This and the amount of sequence divergence indicate possible cryptic speciation in its endemic host, the Lerma catfish, Ictalurus dugesi.

Phylogenetic Relationships of North American Field Crickets Inferred from Mitochondrial DNA Data

A well-supported molecular phylogeny for North American Gryllus species based on a combined data set of mitochondrial (mt) DNA is presented. A total of 26 individuals representing 13 populations of 11 species of the genus Gryllus and 4 individuals of two outgroup species, Teleogryllus oceanicus and Acheta domestica, were sampled in this study. The complete cytochrome b gene (1036 bp) and a 500-bp fragment of the 16S rRNA gene were sequenced for each individual. Since results from separate analyses of the cytochrome b and 16S data sets, as well as a previously published mtDNA restriction-site data set, were not conflicting, all data were combined for phylogenetic analyses. The clade of European Gryllus was clearly separated from the North American clade. The amount of sequence divergence between these clades was significantly greater than within the clades, suggesting a basal drift-vicariant event in the genus. This is the first phylogenetic analysis of North American Gryllus that includes western species. Four well-supported groups were identified but their relationships showed no clear east-west structure. Our phylogeny supports the recent reassignment of G. integer Scudder 1901 from Texas to G. texensis Cade and Otte 2000. The evolution of cricket song and life cycle is discussed using the new phylogenetic framework.

What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree.

The cnemophiline 'birds of paradise' (Cnemophilinae) and Macgregor's 'bird of paradise' (Macgregoria) have traditionally been included in the Paradisaeidae although their relationships within the group have been enigmatic and subject to repeated discussion in the literature. Here we use sequences from two mitochondrial genes, cytochrome b and cytochrome oxidase I, along with a suite of morphological characters, to investigate their relationships to paradisaeids and other members of the passerine Parvorder Corvida. The combined data strongly support the removal of both groups from the birds of paradise: the cnemophilines are basal members of the Corvoidea and Macgregoria is a member of the Meliphagoidea and embedded in the honeyeaters (Meliphagidae) close to the genus Melipotes. The amount of sequence divergence among basal passeriforms and members of the Corvida, as well as available fossil evidence for Australian corvidans, suggest that cnemophilines represent an ancient lineage within the corvoid radiation. Because cnemophilines and Macgregoria have been placed at the base of the paradisaeid tree, hypotheses of morphological, behavioural and ecological character-state transformations within the family will require reanalysis.

Sequence analysis of NSP4 gene of human rotavirus allows classification into two main genetic groups

The rotavirus nonstructural glycoprotein NSP4 may represent the first identified viral enterotoxin. We have sequenced reverse transcription-polymerase chain reaction (RT-PCR)-generated fragments of 16 NSP4 genes of human rotavirus (HRV) strains from six different countries, representing seven different G and P type combinations. Based on the amount of sequence divergence between these and 11 previously sequenced NSP4 genes of human and animal rotaviruses, three distinct genetic groups could be recognized. Most strains within a group were closely related to each other at the nucleotide (nt) and amino acid (aa) levels (usually <10% divergence) but more distantly related (maximum 30.0% nt divergence and 24.7% aa divergence) to members of the other groups. Intergroup variation occurred in two highly variable regions of NSP4 (aa 16-34 and aa 131-148). The NSP4 "toxic peptide" (aa 114-135) exhibited aa variation at its carboxy terminus both within and between genetic groups. The largest group (genetic group II) contained HRV strains of subgroup II specificity (including genotypes P[8]G1, P[8]G3, P[6]G3, and P[8]G5 and serotype P8[11]G9), and the smaller group (genetic group I) contained HRV strains of subgroup I specificity (genotype P[4]G2). The NSP4 sequence of the rhesus rotavirus vaccine strain was distinct from all other strains and formed the third group (genetic group III). The NSP4 genes of animal rotaviruses UK, NCDV, and SA11 (genetic group I) and YM (genetic group II) and two possible human-animal rotavirus reassortant strains, Brazilian P[8]G5 and Indian P[11]G9 (genetic group II), could also be classified into one of these groups, suggesting a close evolutionary relationship between human and animal NSP4 genes. These results will facilitate studies of the host immune response to NSP4, which may be relevant to future HRV vaccine design.

Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles, songs, and habitat associations

AbstractNorth American field crickets (genus Gryllus) exhibit a diversity of life cycles, habitat associations, and calling songs. However, patterns of evolution for these ecological and behavioral traits remain uncertain in the absence of a robust phylogenetic framework. Analyses of morphological variation have provided few clues about species relationships in the genus Gryllus. Here we use comparisons of mitochondrial DNA restriction site maps for 29 individuals representing 11 species (including potential outgroups) to examine relationships among eastern North American field crickets. Initially chosen as likely outgroup taxa, the two European species of Gryllus do not obviously fall outside of an exclusively North American clade and (based on amount of sequence divergence) appear to have diverged from North American lineages at about the same time that major North American lineages diverged from each other. The egg‐overwintering crickets comprise a strongly supported monophyletic group, but relationships among these three closely related species cannot be resolved. The mtDNA data are consistent with a single origin of egg diapause and do not support a model of recent life cycle divergence and allochronic speciation for Gryllus pennsylvanicus and G. veletis. The two crickets are not sister species, despite remarkable similarity in morphology, habitat, and calling song. This conclusion is consistent with published data on allozyme variation in North American field crickets. The habitat associations of eastern North American field crickets have been labile, but calling songs sometimes have remained virtually unchanged across multiple speciation events.

Affinities of the Hawaiian Goose Based on Two Types of Mitochondrial DNA Data

ABSmAcTr.-We compared restriction fragments of mitochondrial DNA and sequences of portions of the cytochrome b gene of the following: the Hawaiian Goose (Nesochen sandvicensis), five subspecies of the Canada Goose (Branta canadensis), the Pacific Black Brant (B. bernicla nigricans), and the Emperor Goose (Chen canagica). Both comparisons support the association of the Hawaiian Goose and the Canada Goose as sister taxa as well as the association of all four large-bodied subspecies of Canada Geese as separate from the one small-bodied subspecies analyzed here. Bootstrap and winning-sites tests show these associations to be statistically significant. The amount of sequence divergence implies that Hawaiian and Canada Geese diverged from a common ancestor less than three million years ago and that this divergence preceded the divergence of largeand small-bodied Canada Geese only slightly, if at all. Therefore, we suggest a North American origin for the Hawaiian Goose. Received 2 July 1990, accepted 27 December 1990.

Evolutionary divergence between sympatric species of southern African Hakes, Merluccius capensis and M. paradoxus. II. restriction enzyme analysis of mitochondrial DNA

We used 11 restriction endonucleases to measure nucleotide sequence variation in mitochondrial DNA (mtDNA) within and between two species of hake from the coastal waters of South Africa. A total of 14 different composite genotypes were observed among 26 individuals of Merluccius capensis, but only 6 composite genotypes were observed for 24 individuals of M. paradoxus. A parsimony network connecting the composite genotypes for these species did not correspond with the geographies of either set of samples. In M. capensis, the restriction patterns of three enzymes (Ava I, Xba I, Xho I) and the network of composite genotypes indicate that an addition of about 400 nucleotides in length and a deletion of 200 nucleotides have occurred in pathways leading from the most common genotype. The amount of nucleotide site polymorphism for M. capensis was 0·022 and was significantly greater than the level of polymorphism in M. paradoxus, which was 0·009. These results suggest that M. paradoxus may have experienced a population bottleneck in the past. The amount of sequence divergence between these species was 11·6 per cent (±0·036) and is typical for well differentiated species. Using the assumptions of the molecular clock, this represents a divergence time of 5·8 (±1·8) million years.