A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at https://github.com/rachelss/SISRS.Comment: 12 pages plus36 figures, 1 supplementary table, 3 supplementary figure

A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

The Grizzly, March 21, 2002

Wynton Marsalis Brings Down the House at Ursinus • The True History of St. Patrick\u27s Day • Music Series set for Berman Museum • Ursinus Women\u27s History Month Dedicated to Late Professor • Meistersingers to Perform at Ursinus College • Berman Museum of Art to Feature Hans Moller Retrospective • SERV and Campus Safety to the Rescue • The New Fad Drug that Might be a Thinly Veiled Disaster • Girls Lacrosse Starts out Strong after a Productive Southern Swinghttps://digitalcommons.ursinus.edu/grizzlynews/1510/thumbnail.jp

COVID-19 and OD: Unplanned Disruption and the Opportunity for Planned Talent Development

COVID-19 created an unprecedented global health crisis and caused a rapid, global economic meltdown. Organizations of all sizes are scrambling to salvage workforces and adopting policies to protect employees from the virus. Talent development practices face new challenges as the world reckons with our altered COVID-19 pandemic reality. Organization leaders must think creatively to design the employment practices of the future. In this article, we consider how changes in work environments affect employees and organization performance, examine how recruitment, training, onboarding, and developing talent present complex challenges that must be addressed for sustainability, and consider how talent development principles can enhance OD practices. Finally, we offer perspectives on employing OD principles and practices to facilitate workforce changes to maximize productivity and performance

The Grizzly, April 4, 2002

Ursinus Students Seek an International Perspective During Model U.N. • Airband: When Your Lip-syncing Actually Helps Save a Life • Binge Drinking: When College Becomes Equivalent to the Neighborhood Bar • The Class of 2002 gets Ready for the Senior Class Gift Drive • Opinions: Want Easter Vacation? Some Schools Have it • Performer Gives Life to Short Stories of the South • Softball Turning Around for Some Wins • Comparative Pricing Report: Pedicureshttps://digitalcommons.ursinus.edu/grizzlynews/1512/thumbnail.jp

The Grizzly, May 3, 2001

Xenadrine Evidence Points Towards Addictive Nature • Class of 2004 Offers Words of Wisdom to Class of 2005 • Public Radio Personality Ira Glass Hosts Lecture at Ursinus • Fountain Expected to be Completed Soon • Saying Goodbye: Grizzly Editor Signoffs • Opinions: National Missile Defense Still a Bad Idea; Greek Week Unites Local Organizations; Awards Ceremony an Enriching Experience • Stalin\u27s Daughter Steals the Stage • Annual Student Art Show Arrives at Berman • Women\u27s Lacrosse Wins CC Title; Looks Ahead to NCAA\u27s • Girls Rugby Finishes Spring Season • Tennis Teams Lose in First Round at CCC • A Weekend of CCC Playoffs and Tournaments Sees Success for Few • Final Exams Schedulehttps://digitalcommons.ursinus.edu/grizzlynews/1490/thumbnail.jp

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes?7 of which are novel?from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g fromEarly andMiddle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal 15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement 9,000 years ago.Fil: Roca Rada, Xavier. Centre For Ancient Dna, University Of Adelaide; AustraliaFil: Politis, Gustavo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Messineo, Pablo Geronimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scheifler, Nahuel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scabuzzo, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Entre Ríos. Universidad Nacional de Entre Ríos. Centro de Investigaciones y Transferencia de Entre Ríos; ArgentinaFil: Gonzalez, Mariela Edith. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Harkins, Kelly M.. University of California; Estados UnidosFil: Reich, David. Harvard Medical School; Estados UnidosFil: Souilmi, Yassine. University of Adelaide; AustraliaFil: Teixeira, Joao C. T.. University of Adelaide; AustraliaFil: Llamas, Bastien. University of Adelaide; AustraliaFil: Fehren Schmitz, Lars. University of California; Estados Unido

The Grizzly, March 28, 2002

Six Months after 9/11: Has America Really Changed? • The Ursinus Hillel Celebrates Passover • Valedictorian and Salutatorian Announced for 2002 • Room Lottery Returns to Ursinus • Omega Chi Blood Drive a Huge Success • First Ursinus Watson Fellow: Aaron Ranck to Study Agrarian Life • Post Traumatic Stress Disorder on the Rise • Opinions: Do Greek Organizations Foster Group Think ?; Educational Philosophy of Ursinus College • Women\u27s Lacrosse Continues to Tear Through their Schedule • Gymnastics Brings Home Fourth at the NCGA • Performance Enhancing Drugs Back in the Spotlight • Gymnastics Results • Bears Split with Red Devils in First Game of Conferencehttps://digitalcommons.ursinus.edu/grizzlynews/1511/thumbnail.jp

The Grizzly, April 18, 2002

From the B-52\u27s to the Beach Boys: Airband was a Huge Success • ProTheatre Stages History with Twilight: Los Angeles this Weekend • Students Rave About the Pat McGee Band in Concert • Adolph Reed to Deliver Pancoast Lecture • Fitness Week a Fitness Blast • Male Birth Control: Latest Medical Breakthrough? • Opinions: Greek Portrayal in Movies Demeaning, not True!; Parking Policy not Fun for Some Residents • Y100\u27s Caseyboy and his Crazy Stunts • The Letters and the Cane • Comparative Pricing Report: Self Tanners • Skin Cancer is not Your Friend • UC Women\u27s Rugby Making a Breakthrough in Women\u27s Sports • Workman\u27s Workouts Paying Off for Field Hockey • Baseball Team Winds Down Season Looking for Top Spot in Centennial Conference Playoffs • Erin Fitzgerald Named Centennial Conference Women\u27s Lacrosse Player of the Week • Dougherty Qualifies in 5000m for NCAA Championships • Another Flawless Season for Women\u27s Lacrosse to Lead Team to Second Consecutive Championship Title • UC Men\u27s LAX Stars: What are they up to Now? • Win, Loss, and Postponement for UC Softball as Season Winds Downhttps://digitalcommons.ursinus.edu/grizzlynews/1514/thumbnail.jp

The Grizzly, February 21, 2002

Former U.S Ambassador to Sierra Leone now Ursinus Professor • Professor Melrose Testifies Before the Senate • Fire in Reimert: Where Were the Smoke Detectors? • Grant Will Enhance Ursinus Asian Studies Program • Marisol: A Lesson in Living in the Aftermath of September 11th • Winter Olympics Take Salt Lake by Storm • Save a Life: Donate Blood at the March Blood Drive • Opinions: Dressing Up: What Happened to Everyone\u27s Style?; Heart-wrenching and Heart-warming Olympics; For the Appropriateness of Fraternities and Sororities on Campus • When Making Love Becomes Sex: Diversifying Love and Sex • Price Comparison: Don\u27t Let the Cold Season Hurt Your Wallet • Pledging in the Past • Women\u27s Basketball Shoots Out Bryn Mawr to end 2002 Season • Men\u27s Basketball Looks Toward Showdown with Franklin & Marshall • Centennial Conference Wrestling Tournament Held at Ursinushttps://digitalcommons.ursinus.edu/grizzlynews/1508/thumbnail.jp