Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

BACKGROUND: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale. RESULTS: We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart. CONCLUSIONS: Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates

The Grizzly, December 7, 2017

Local Christmas House Brings Students Cheer • UCARE Giving Tree Brings Joy and Gifts to Local Children • Sharing the Story of the Miracle of Chanukkah • Alumni Invited to Wreath Laying at Arlington National Cemetery • Ursinus Students Celebrate the Holidays • Prepare Your Stomach for the Holidays • Opinions: Happy Holidays vs. Merry Christmas; Grizzly\u27s Holiday Polls • Proficiently Efficient: Men\u27s Basketball is 4-2 • UC\u27s Swim Teams Make Waveshttps://digitalcommons.ursinus.edu/grizzlynews/1634/thumbnail.jp

The Grizzly, May 9, 2019

Kingston Out, Varner in for Bear Bash • Ursinus Reacts to Symbol of Hatred • Q&A with President Blomberg • Ursinus Graduates First Wave of Education Studies Majors • Breakaway Student Productions\u27 One Act Festival Premieres Four Student-Written Plays • Ursinus Fulbright Scholar, Jason Bennett \u2719, to Research Theoretical High-Energy Physics at the University of Groningen in the Netherlands • Opinions: Swarthmore Scandal Speaks to Greater Issues with Fraternity Culture; The United States Should Shorten its Work Week • Athlete Spotlight: Running Back Sam Ragland \u2721 • The Thanks for a Fun Two Years Award: You, the Fans • Bears Win Conference Championshiphttps://digitalcommons.ursinus.edu/grizzlynews/1622/thumbnail.jp

The Grizzly, November 1, 2018

Midterm Elections November 6 • IDC Opening Honors Past President Fong, Celebrates Campus Milestone • Deadline for The Lantern is Here • Board of Trustees Comes to Campus • Geology Professors go Under the IDC • Meet the Charles Rice Post-Graduate Research Fellows • Opinions: Kavanaugh and the Powers of the Supreme Court; Is the New UC Tour Guide Dress Code Sexist? • Women\u27s Swimming Begins Title Defense with Back-to-Back Dual Meet Wins • Senior Bridget Sherry Nominated for NFHCA Senior Game as Field Hockey Preps for Post-Seasonhttps://digitalcommons.ursinus.edu/grizzlynews/1606/thumbnail.jp

The Grizzly, September 28, 2017

Constitution Day Sparks Student Discussions of Free Speech • Chin Brings Sexy Bad Girl Haikus, Asian American Blues Poems and Elegies to Ursinus Reading • Next Year\u27s Study Abroad Application Opens on October 3rd • Armstrong Lecture Brings Columbia University Historian Dr. Joshua Batts to Berman Museum • Home is Where the Bear is • New Species Comes to Ursinus • Opinions: Consciousness Raising Can Combat Rape Culture on Campus; Is This Sufjan Stevens Song Gay or Just About God? • Student Workers of the SMC • Pair of Wins Put Bears in Good Positionhttps://digitalcommons.ursinus.edu/grizzlynews/1626/thumbnail.jp

The Grizzly, October 26, 2017

History of Halloween • Senior English Majors go Gothic • SAO Plans Halloween Trip to Dorney • Senior Halloween Party: An Ursinus Tradition • Fright Night: Phoenixville Theatre Hosts Horror Film Series • Spooky Ursinus Folk • Something Wicked This Way Comes • Opinions: A Ghost Story Haunts with Quiet Pain and Loss; Trick-or-Treating Should End for Children Older than Thirteen • Superstitions Win Confidence for Ursinus Student Athletes • First Year Athletes Face Scary New Adjustmentshttps://digitalcommons.ursinus.edu/grizzlynews/1629/thumbnail.jp

The Grizzly, September 14, 2017

Three Workers Injured in IDC Construction Accident • Rush Week Comes Early This Year • Have You Seen Scene / Unseen? • Ursinus Welcomes a New AD to Main Street • A Fairy Tale in the English Department • Opinions: Trump\u27s Move to End DACA is One of his Most Disgusting Acts Yet; Why Resident Advisers Could Benefit From a Union • Fresh Voice for UC Volleyball • Bears Beat Bison and Bullets for Hot Start to Seasonhttps://digitalcommons.ursinus.edu/grizzlynews/1624/thumbnail.jp

The Grizzly, November 9, 2017

Department of Education Rolls Back Piece of Title IX • Joe DeSimone \u2786 Receives Heinz Award • New Education Major Created • Nadler Awarded Tow Fellowship • Dr. Kerr Appears on Full Frontal with Samantha Bee • History of a Historian • Opinions: Male Gun Violence Must End with Restrictive Gun Legislation; JFK\u27s Legacy Should be More Than Assassination Conspiracies • Senior Athletes Share Memories as Fall Sports Seasons Wind to a Close • Football Drops Three of Last Four Gameshttps://digitalcommons.ursinus.edu/grizzlynews/1631/thumbnail.jp

The Grizzly, October 5, 2017

The Fringe Festival Returns to Ursinus • U-Imagine Hosts Marketing Contest • UCARE Holds Voter Registration Drive and Local Election Panel • Q&A with Aneesah Smith: Ally Training Facilitator • Breaking Through the Haze • Perspective from the Past • Opinions: NFL Players Take a Knee to Stand up Against Injustice; Recent Natural Disasters Demand More Human Decency • Moving the Chains: Inside Look at the UC Chain Gang • UC Swimming Dives in for Midnight Madnesshttps://digitalcommons.ursinus.edu/grizzlynews/1627/thumbnail.jp