Occurrence and implicatons of biological network evolution following polyploidy

The mapping and comparison of biological networks allows for analysis to understand forces of evolution. Here, we synthesize information about polyploidy, or whole genome duplication, and its effects on network rewiring. Network changes may have lead to the diversity and survival of some lineages of life, and by understanding network evolution, we may discover patterns that explain how organisms evolve. Specifically, we focus on the consequences of polyploidy on flowering time. Our work aids those studying different aspects of polyploidy to see a bigger picture of how it contributes to evolutionary change and important features that may be involved in cancer. Future studies of biological networks will help improve models of disease and biological processes to make better crops for food, fuel, fiber, and pharmaceuticals

Characterization of a recombinant inbred line population for quantitative trait locus mapping

Abstract only availableEukaryotes can regulate gene expression by epigenetic mechanisms at the chromatin level. One epigenetically regulated gene in maize is Pl1-Blotched, an allele of purple plant1, which activates anthocyanin pigment production. Normally, Pl1-Blotched leads to a variegated pattern of pigmentation, but its pigment level can be increased by a modifier called Suppressor of plant blotching (Spb). At the molecular level, Spb alters the chromatin packing of Pl1-Blotched, leading to less tightly packed chromatin and higher gene expression. The genetic identity of Spb is not yet known, although preliminary results indicate the Spb-enhanced pigment phenotype is a quantitative trait. As a step toward isolating the genes for Spb, a mapping population of Recombinant Inbred Lines (RILs) was generated by inbreeding the progeny of an F2 derived from a cross of Pl1-Blotched with Spb to a less pigmented Pl1-Blotched stock. Genotypes were determined for 188 RILs using microsatellite or simple sequence repeat (SSR) markers. RILs were evaluated for residual heterozygosity, breakpoint locations, and heterozygous chromosomal positions. A map was created and will be used as the foundation for mapping Spb and for estimating the heritability of the Spb phenotype.NSF-REU Program in Biological Sciences & Biochemistr

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Background Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats. Results New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya. Conclusions Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.This work was supported in part by the Plant Molecular Biology Center, the Department of Biological Sciences at Northern Illinois University and the National Science Foundation under Grant Numbers DEB-1120750 to LGC, DEB-1120856 to SAK and DEB-1120761 to MRD.This article is made openly accessible in part by an award from the Northern Illinois University Libraries’ Open Access Publishing Fund

Arctos: A Tool to Help Small Collections Make Their Case

Part of SPNHC 2019 | https://osf.io/view/SPNHC201

The evolution of Western tonality: a corpus analysis of 24,000 songs from 190 composers over six centuries

The corpus of Western music offers the chance to analyze trends in its evolution. Here, we analyze greater than 24,000 MIDI (Musical Instrument Digital Interface) transcriptions of Western classical music from 197 composers spanning from the 15th to 20th centuries. The unique file format of MIDI files (notes of discrete frequencies turning “on” and “off” at specific times) allows us to statistically quantify note usage with respect to pitch class and intervals. We first perform a Principal Component Analysis (PCA) on pitch class and show that the data creates a ring. Songs strongly associated with a particular key fall on the ring, whereas highly chromatic and atonal works fall in the center, revealing that the evolution of Western music is constrained by the circle of fifths. We then examine interval usage. Discriminant analysis on composer identity reveals that a major source of evolutionary change is incremental and linear. Interval usage predicts individual composer identity at levels above chance. A Self-Organizing Map (SOM) reveals four major groups of composers with similar tonal styles. These groups are loosely based on traditional musical eras, but reveal unexpected continuity between co-existing schools of composers

Secondary Structure Analyses of the Nuclear rRNA Internal Transcribed Spacers and Assessment of Its Phylogenetic Utility across the Brassicaceae (Mustards)

<div><p>The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships.</p></div

Phylogenetic Distribution of Hairpin Numbers for ITS Secondary Structures.

<p>A tribal level phylogeny of the Brassicaceae, strict consensus tree of the 200 most parsimonious trees estimated with ITS sequences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101341#pone.0101341-Warwick1" target="_blank">[2]</a>, was utilized to investigate the evolution of the number of hairpins present in the secondary structures of both ITS1 and ITS2. Bootstrap support values greater than 60% are shown above branches <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101341#pone.0101341-Warwick1" target="_blank">[2]</a>. It is notable that the ITS tree does neither fully reflect the tribal phylogeny nor is at any deep node highly significantly supported, but overall-topology is in congruence with multi-locus phylogenies considering major lineages <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101341#pone.0101341-Beilstein2" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101341#pone.0101341-Couvreur1" target="_blank">[8]</a>. Tribes not assigned to one of the three major lineages are actually combined with an "expanded lineage II" <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101341#pone.0101341-Franzke2" target="_blank">[46]</a>, which might have to be revised in future. The three major phylogenetic lineages are shown within colored blocks with Lineage I (orange), Lineage II (blue) and Lineage III (green). The number of hairpins for each secondary structure is shown at the phylogenetic tips with 3 (orange boxes), 4 (yellow boxes), 5 (green boxes), 6 (blue boxes), and 7 (purple boxes). Tribes with a lack of available complete ITS1 data are marked as 'NA'. Tribes with secondary structures with different number of total hairpins from different species are also indicated (e.g. Camelineae 6/7 for ITS1; 6 and 7 hairpin structures are observed) within the colored box of the fewest hairpined structure. Examples of secondary structures are shown (top-bottom order): 1. <i>Anchonium billardierei</i> ITS1 (Anchonieae), 2. <i>Aethionema arabicum</i> ITS1 (Aethionemeae), 3. <i>Halimolobos lasiolaba</i> ITS2 (Halimolobeae), and 4. <i>Arabis scabra</i> (Arabideae).</p

Comparison of Secondary Structures of 100 ITS and 100 Random Sequences.

<p>A scatter plot of the lowest energy state values (x-axis) and all possible secondary structures (y-axis) for 50 ITS1 (Blue Diamonds), 50 ITS2 (Red Squares) and 100 randomly generated sequences (Green Triangles) (Supplemental File 1) estimated using RNAstructure 5.3 (Reuter and Mathews, 2010).</p