Evolutionary Genomics

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have higher transposon density (25%-50%) than euchromatic reference regions (3%-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% versus 11%-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density ...

We present a comprehensive compilation of genomic structure evolution that should help the reader that is not familiarized with genomics to understand the mechanisms that are shaping its structures over time. We believe that this understanding is essential to work with genomics in the sense that it should help to formulate productive hypothesis for new original works. We believe that the mechanism by which the extant genomic structures arose is more important that the shape of these structures since evolution is continuously at work. In addition, taking genomics under the evolution perspective gives the possibility to release a unified picture to the reader of the unlimited natural complexity without fair to be incomplete. It is amazing to relize how fast complex biological structures arose in the early time of earth and we tried to give this constructive view to the reader.

We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from control genes or cenes. Cenes are interpreted and executed by the cell and, thereby, direct cell actions including communication, growth, division, differentiation and multi-cellular development. The cenome is the global developmental control network in the genome. The cenome is also a cene that consists of interlinked sub-cenes that guide the ontogeny of the organism. The complexity of organisms is linked to the complexity of the cenome. The relevance to ontogeny and evolution is mentioned. We introduce the concept of a universal cell and a universal genome.

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However,
all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa
dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

The key to the keys to immortality and eternal youth lies in the correct answer to the main question: How to naively discover new essential – but still hidden – features required for properly training novel adaptive supervised machine learning algorithms (SMLA)

This is the abstract for The Parrish Lecture that was held at Kansas State University on Tuesday, 13 April 2021. Sponsored by the Kansas State University History Department, this talk offered a summary of the state of research on the global history of plague, a disease associated with at least three historic pandemics and one whose investigations--by both scientists and humanists--offers us the best model for studying the natural and cultural processes that produce pandemic events in the modern world.

A recording of the talk is now available at this link: https://mediasite.k-state.edu/mediasite/Play/897bddc6b31e43b8aa161ade20f01a171d.

Polyploid genomes evolve and follow a series of dynamic transfigurations along with adaptation and speciation. The initial formation of a new polyploid individual within a diploid population usually involves a triploid bridge, a two-step mechanism of cell fusions between ubiquitous (reduced) and rare (unreduced) gametes. The primary fusion event creates an intermediate triploid individual with unbalanced genome sets, a situation of genomic-shock characterized by gene expression dysregulation, high dosage sensitivity, disturbed cell divisions, and physiological and reproductive attributes drastically altered. This near-sterile neotriploid must produce (even) eupolyploids through secondary fusion events to restore genome steadiness, meiotic balance, and fertility required for the demographic establishment of a nascent lineage. Natural conditions locate several difficulties to polyploid establishment, including the production of highly unbalanced and rarely unreduced (euploid) gametes, frequency-dependent disadvantages (minority cytotype exclusion), severe fitness loss, and ecological competition with diploid parents. Persistence and adaptation of neopolyploids depend upon genetic and phenotypic novelty coupled to joint selective forces that preserve shock-induced genomic changes (subgenome homeolog partitioning) and drive meiotic (reproductive) stabilization and ecological diversification. Thus, polyploid establishment through the triploid bridge is a feasible but not ubiquitous process that requires a number of low-probability events and singular circumstances. Yet, frequencies of polyploids suggest that polyploid establishment is a pervasive process. To explain this disparity, and supported in experimental evidence, I propose that situations like hybridization and ploidy-state transitions associated to genomic shock and substantial developmental alterations can transiently activate apomixis as a mechanism to halt genomic instability and cancel factors restraining neopolyploid's sexual fertility, particularly in triploids. Apomixis –as a temporal alternative to sex– skip meiosis and syngamy, and thus can freeze genomic attributes, avoid unbalanced chromosomal segregation and increase the formation of unreduced euploid gametes, elude frequency-dependent reproductive disadvantages by parthenogenetic development of the embryo and permissive development of endosperm during seed formation, and increase the effective population size of the neopolyploid lineage favoring the formation rate of eupolyploids compared to aneuploids. The subsequent action of genome resilience mechanisms that alleviate transcriptomic shock and selection upon gene interactions might restore a stable
meiosis and sexual fertility within few generations, as observed in synthetic polyploids. Alternatively, provided that resilience mechanisms fail, the neopolyploid might retain apomixis and hold genomically and transcriptionally altered states for many generations.

Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawaiʻi, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability.

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, andmany Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We
find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.

The clade of the North American lizard genus Sceloporus and its relatives comprising the subfamily Phrynosomatinae (Iguanidae) include perhaps 150 evolutionary lineages. The work reviewed here begins with the discovery more than 40 years ago of the concentration of Robertsonian chromosomal variability in Sceloporus and cytogenetic and genomic evidence of remarkable chromosomal variation within the S. grammicus complex associated with narrow zones of hybridization between different chromosomal races. These discoveries led to hypotheses about hybrid zones involving negative heterosis, possible modes of chromosomal speciation, and the potential roles of such speciation in phylogenesis. The radiation of Sceloporus has now been studied by many different workers extending and mapping the geographic distribution of cytogenetic and genomic variation to understand the biology of the chromosomal variation and to establish the phyletic relationships of the various lineages. The result is a robust phylogeny and a large and still growing database of genic, cytogenetic and other biological parameters. These materials provide a rich series of natural experiments to support both synthetic-comparative and analytical studies of the roles of chromosomal variation, hybrid zones and modes of speciation in phylogenesis and evolutionary success.

The microbiota i.e. all those good bacteria along our intestines, influencing the maturation of the immune system, affects our health and well-being and protect us from diseases such as allergies, diabetes and even cancer. That's why we often hear talk about the microbiota. It all starts with the birth, (eutocico) and during vaginal passage, begins the exchange of bacteria that will colonize the intestines of the unborn child and be able to educate the immune system to recognize what belongs all body (self), from what is foreign (non-self). It will speak, therefore, tolerance of immunological, this phenomenon will continue with the breast feeding and the exchange with the saliva of the mother. We can say that the microbiota of the mother, closely related to food choices, it is essential for proper immune development of their child, then why not pay attention all the nutrition during pregnancy?

De novo genome and transcriptome data from a number of marine algal species have recently become available, ranging from red, green and brown algae, as well as other photosynthetic eukaryotes, e.g. diatoms and dinoflagellates. Phylogenomic approaches are widely adopted to decipher the evolutionary relationships among diverse lineages. Novel algal genomes therefore provide an exciting analysis platform for understanding algal biology, ecophysiology and diversity, and at a broader scale, eukaryote evolution. In this brief communication, I highlight major findings from recent phylogenomic studies of marine algae and their impact to the research field. I discuss the current trends and future directions of phylogenomics, and how we can apply this approach in studying marine diversity in the South China Sea.

Background: The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and
coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and
mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific
nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates
supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization
of chromatin in early genomes.
Results: We have mapped nucleosome positions in T. brucei and identified important differences compared to other
eukaryotes: The RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion,
and show little evidence for defined −1 and +1 nucleosomes. In contrast, a well‑positioned nucleosome is present
directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were
depleted of nucleosomes, with a single well‑positioned nucleosome present immediately downstream of the pre‑
dicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays
of well‑positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves
exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared
with replication origins in other chromosomal core regions.
Conclusions: Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may
already have been present in the last eukaryotic common ancestor.

Imperatively Hidden Objects/Factors (IHO/F) refers to relevant items, which we cannot perceive and measure yet. Nevertheless, they have an impact on our predicted outcome. We have created model that allows for the integration and discovery for the still unknown. If researchers would take the time to understand it, they'd design their experimental studies in a much different way because their scientific objective would shift toward feature discovery to enhance feature selection to make even better predictions with supervised machine learning algorithms.

BACKGROUND: Asthma is a complex disease with striking disparities across racial and ethnic groups, which may be partly attributable to genetic factors. One of the main goals of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to discover genes conferring risk to asthma in populations of African descent. METHODS: We performed a genome-wide meta-analysis of asthma across 11 CAAPA datasets (4,827 asthma cases and 5,397 controls), genotyped on the African Diaspora Power Chip (ADPC) and including existing GWAS array data. The genotype data were imputed up to a whole genome sequence reference panel from n=880 African ancestry individuals for a total of 61,904,576 SNPs. Statistical models appropriate to each study design were used to test for association, and results were combined using the weighted Z-score method. We also used admixture mapping as a complementary approach to identify loci involved in asthma pathogenesis in subjects of African ancestry. RESULTS: SNPs rs787160 and rs17834780 on chromosome 2q22·3 were significantly associated with asthma (p=6 ·57×10−9 and 2·97 × 10−8 respectively). These SNPs lie in the intergenic region between the Rho GTPase Activating Protein 15 (ARHGAP15) and Glycosyltransferase Like Domain Containing 1 (GTDC1) genes. Four low frequency variants on chromosome 1q21.3, which may be involved in the "atopic march" and which are not polymorphic in Europeans, also showed evidence for association with asthma (1·18 × 10−6 ≤p≤3·06 ×10 −6). SNP rs11264909 on chromosome 1q23·1, close to a region previously identified by the EVE asthma meta-analysis as having a putative African ancestry specific effect, only showed differences in counts in subjects homozygous for alleles of African ancestry. Admixture mapping also identified a significantly associated region on chromosome 6q23·2, which includes the Transcription Factor 21 (TCF21) gene, previously shown to be differentially expressed in bronchial tissues of asthmatics and non-asthmatics. CONCLUSIONS: We have identified a number of novel asthma association signals warranting further investigation.

Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven mi-crosatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more dis-criminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.

Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea. D. superbus had the longest large single copy (LSC) region (82,805 bp), with some variations in the inverted repeat region A (IRA)/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryo- phyllaceae family; however, intense variations were not identified. The pseudogene ribo- somal protein subunit S19 (rps19) was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initia- tion factor IF-1 (infA) and ribosomal protein subunit L23 (rpl23) genes were absent from the Dianthus cp genome. When the cp genome of Dianthus was compared with 31 other angio- sperm lineages, the infA gene was found to have been lost in most members of rosids, sola- nales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of Dianthus and Spinacia has two introns in the proteolytic subunit of ATP-dependent protease (clpP) gene, but Lychnis has lost introns from the clpP gene. Furthermore, phylogenetic analysis of indi- vidual protein-coding genes infA and rpl23 revealed that gene loss or pseudogenization occurred independently in the cp genome of Dianthus. Molecular phylogenetic analysis also demonstrated a sister relationship between Dianthus and Lychnis based on 78 protein-cod- ing sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

Mutations are normally classified according to their proximal effect on an organism’s fitness, whether beneficial, deleterious, or neutral. While this is a very useful first-pass categorization of mutations, the realization that mutations are not always haphazard, but in fact may be part of a regulated design, means that creationists should be looking for a deeper classification of mutations based on whether or not they conform to their organism’s design. Design-consistent mutations are those which occur within the pattern expected by the genome’s architecture, and design-inconsistent mutations are those which occur outside of the genome’s architecture. Features such as metabolic consistency, mutational mechanism, mutation rate, reversibility, and preservation of genome semantics can be used by biologists to assess whether or not a mutation is design-consistent or design-inconsistent.

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core-and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating

Please click here http://singledrug.com/media/Temporal_Analysis_of_Aging_description.pdf to see it.

I plan to add the following:

I found Osh6 at a very high rank of lifespan extending genes.  That is why I want to take all the genes that are part of the same molecular function as Osh6 and run an expression similarity analysis on SPELL (Serial Pattern of Expression Levels Locator) (see spell.yeastgenome.org/). 

I hope to find genes of unknown functions that could be involved in the same molecular function.  If I find this, I'll validate with my time series plots and TFBS similarity analysis.  That way I hope to predict the function of an unknown gene in lipid metabolism.  I will also try the opposite approach, i.e. I'll take genes of unknown function and look for a group of similarly expressed genes, which belong to the same GO term.

I added 19 pages to the second chapter.  I was able to further improve the accuracy of my yeast lifespan predicting machine learning algorithm by adding more features about lipids.  My last draft had an average prediction error of +/-5 replications.  Now it is less than +/-3 replication for the 50th percentile of the replicative lifespan.  To my knowledge nobody has published any research on about using machine learning and feature selection to predict the replicative age.

If you have any more ideas how I could make my dissertation look better, I'd be very thankful for any new feasible ideas and inspirations.  I have mainly been using Python and R for all my analysis.

I found that ribosomal RNA and proteins are most closely follow the cell cycle and that if knocked out the yeast's lifespan can be extended significantly.  I want to use the different cyclical periodically recurring and highly fluctuating gene expression oscillation pattern to discover the functions of genes we have not yet discovered.  I am interested in this because a friend of mine showed me a cancer dataset that looked very similar.  Since cancer is very similar to the yeast in that it keeps constantly dividing and hence its age can be expressed in replication we could use the same guilt-by-association approach to infer the functions or at least the way their expression is controlled by TFs from genes with similar temporal expression patterns of genes with already known functions.

When analyzing the time series plots of the 62 yeast chaperons I discovered that their expression plot trajectories can easily be clustered into 7 expression patterns, which are consisted with the 7 classes of yeast chaperons.  If I had only taken the average centroid of all 62 chaperons I would have been misled because using this approach could not be applied to potentially discover more new currently still unknown chaperons because no unknown chaperon would have time series trajectories, which would highly correlate with the average chaperon expression pattern of all 7 classes since their in-group expression pattern is very homogeneous but between the 7 different chaperon classes the expression pattern is very different.

I intended to elucidate the different ways by which we age by a very similar clustering algorithm, which I have developed based on time series curves over three subsequent yeast cell cycle consisting of 36 mRNA measures each about 25 minutes apart; thus, allowing to measure very steep mRNA expression fluctuation periods by manifold within the only 90 minutes of the cell cycle because even very brief but rapid expression changes that last not much longer than 1/12th of a cell cycle, of which I found surprisingly many.

The lined sea anemone Edwardsiella lineata has evolved a derived parasitic life history that includes a novel body plan adapted for life inside its ctenophore hosts. Reputedly its sole host is the sea walnut, Mnemiopsis leidyi, a voracious planktivore and a seasonally abundant member of many pelagic ecosystems. However, we have observed substantially higher E. lineata prevalence in a second ctenophore species, the ctenophore predator Beroë ovata. The interplay among these 3 species has important conservation consequences as M. leidyi introductions are thought to be responsible for the severe depletion of numerous commercial fisheries in the Mediterranean basin, and both E. lineata and B. ovata have been proposed as biological controls for invasive M. leidyi. Over a 3-yr period (2004–2006), we collected 8,253 ctenophores from Woods Hole, Massachusetts, including M. leidyi, B. ovata, and a third ctenophore, Pleurobrachia pileus, and we recorded E. lineata infection frequencies, parasite load, and parasite location. We also conducted laboratory experiments to determine the likely mechanisms for parasite introduction and the effect of each host on parasite development. We observed peak E. lineata infection frequencies of 0% in P. pileus, 59% in M. leidyi, and 100% in B. ovata, suggesting that B. ovata could be an important natural host for E. lineata. However, in laboratory experiments, E. lineata larvae proved far more successful at infecting M. leidyi than B. ovata, and E. lineata parasites excised from M. leidyi exhibited greater developmental competence than parasites excised from B. ovata. Although we show that E. lineata is efficiently transferred from M. leidyi to B. ovata when the latter preys upon the former, we conclude that E. lineata larvae are not well adapted for parasitizing the latter species and that the E. lineata parasite is not well adapted for feeding in B. ovata; these developmental and ecological factors underlie the host specificity of this recently evolved parasite.