PI Sethuraman was at the PEQG 2022 meeting in Pacific Grove, CA to present the lab's recent work describing the multinomial clustering method for estimating population genomic structure from polyploid, multi-allelic genomic data. Watch for the preprint describing MULTICLUST! Meanwhile, the tool is accessible via GitHub here.
We are so proud of our lab's three graduates from the Class of 2022 - Robert Reyes, Walker Welch, and MJ Lee! Congratulations and we can't wait to see what amazing things you will go on to do!
Our manuscript that describes the genome of a novel Sediminibacterium discovered in association with two separate cyanobacterial isolates from freshwater locales in Southern California has now been accepted at G3! All the analyses for this manuscript were performed by our super talented NSF REU scholars (including the Sethuraman Lab's very own Andrew Zhang), and the entire paper was written by all of us in a conference room, masked, with everyone contributing sentences - the most unique experience of all! Read the preprint here, while we await the print version!
Our manuscript detailing the changes in microbial diversity and community composition in response to chronic nitrogen input using a long-term experiment has now been published in Applied Soil Ecology! We discovered that soil inorganic nitrogen and pH were prominent predictors of microbial abundance - all work led by Tim Grant from CSUSM. Read more here.
Mean (±SE; n = 4 plots/treatment) sequence counts for Proteobacteria (Pro), Actinobacteria (Act), Bacteroidetes (Bac), Firmicutes (Fir), Acidobacteria (Aci), Verrucomicrobia (Ver), Planctomycetes (Pla), and Chloroflexi (Chl) bacterial phyla in coastal sage scrub (CSS) exposed to ambient (control) and elevated N (N) during the spring (green) and fall (brown). Also shown are results of a two-way ANOVA or permutation test with 1 factor and 12 error degrees of freedom (p-value only) for effects of treatment (N), season (S), and their interaction (N × S). NS = not significant (p > 0.05).
Several of our Sethuraman Lab members presented their research at the SDSU Student Research Symposium on Friday, 3/4/2022 at Montezuma Hall. Congrats to everyone on presenting all the fun science!
The first chapter from Alicia's Masters thesis describing the genome of the parasitoid wasp Dinocampus coccinellae and comparative phylogenomics of hymenopterans has now been published in G3! Our study determined extensive duplications, increased rates of gene gain/loss along the D. coccinellae lineage, along with re-affirming multiple independent origins of eusociality and thelytokous parthenogeny among hymenoptera. Read the full paper here. Congratulations to all Sethuraman Lab students who were instrumental in this publication!
Also, this stunning image showing a larval D. coccinellae egressing from an adult Coccinella septempunctata captured by Roxane Saisho is now featured on the cover of the March 2022 issue of G3! Check out the entire issue here.
Dr. Sethuraman was recently featured on the latest edition of UC Merced's RadioBio podcast where he talks about his work on ghost populations, and population genomics of biological control. Give it a listen here!
The Sethuraman Lab recently joined the Evolutionary Biology group at SDSU - special thanks to Dr. Kevin Burns and his partner for hosting a welcome party at their place. We look forward to years of fun science and collaboration with the team!
We are actively recruiting TWO PhD students via the Joint Doctoral Program in Evolutionary Biology at SDSU (collaboratively offered with University of California Riverside), and TWO Masters students via the Biological and Medical Informatics Graduate Program at SDSU, both starting Fall 2022.
Dr. Sethuraman will work with all graduate students to develop their project(s) which can broadly span the fields of genomics, bioinformatics, and evolutionary biology.
Please write to Dr. Sethuraman (firstname.lastname@example.org) with a copy of your CV/Resume, a brief statement of interest, and let’s chat more.
We are committed to recruiting a diverse group of scientists to join my lab group – so we highly encourage folks who identify as a part of historically underrepresented groups to apply. This includes (non-exhaustively) people of color, international students, Veterans of armed forces, student-parents/caregivers, first-generation degree holders, the LGBTQIA+ family, and folks with medical conditions and disabilities.
Description of Doctoral positions
Start Date: Fall 2022
Application Deadline: December 15, 2021
A Bachelors or Masters degree in Biology/Bioinformatics/Genetics/Computer Science/Statistics, or a related field. Knowledge and experience in scientific programming using C/C++/Python is highly encouraged, but not necessary.
As of 2020, the GRE is no longer required for admissions to the program, but international students are required to submit scores from the TOEFL. More information about admission requirements and procedures can be found at: http://www.bio.sdsu.edu/eb/jdapplications.html
Position 1: Funded by NSF CAREER #2042516 to PI Sethuraman
We currently have an opening for a PhD student (with research funding for ~5 years) to work on projects developing new statistical methods, software, and pipelines for estimation of population structure, relatedness, and evolutionary history from large scale population genomic data while accounting for missingness. Specifically, we will address missingness due to (1) genotyping/variant calling errors, (2) allele dropout in genotyping by sequencing methods – e.g. RADseq, and (3) gene flow from unsampled “ghost” populations.
Position 2: Funded by NIH R15 #1R15GM143700-01 to PI Sethuraman
This PhD student (with research funding for ~5 years) will work on projects in human population genomics, focused on developing new statistical methods, software, and pipelines for analyses of large scale human genomic data to (1) accurately estimate population structure in the presence of archaic gene flow, (2) analyze large human genomic datasets to quantify archaic variation, and (3) understanding patterns of natural selection and adaptation at introgressed archaic variants and haplotypes across humans.
Description of Masters positions
Start Date: Fall 2022, and subsequent Fall terms
Application Deadline: March 1, 2022
A Bachelors degree in Biology/Bioinformatics/Genetics/Computer Science/Statistics, or a related field. As of 2020, the GRE is no longer required for admissions to the BMI program. More information about admission requirements and procedures can be found at: https://informatics.sdsu.edu/admissions/.
We are looking to recruit TWO enthusiastic Masters students to work on various population genomics projects.
Current “Wet” Lab Projects
1. Population genomics of invasive lady beetles (Coleoptera: Coccinellidae)
2. Evolutionary history of domestication of hops (Humulus lupulus)
Current “Dry” Lab Projects (Data Analyses)
3. Annotation, phylogenomic history using the genome of the convergent lady beetle (Hippodamia convergens)
4. Population genomics of a parthenogenetic parasitoid wasp, Dinocampus coccinellae using Ultra Conserved Elements
5. Population genomics of several other species of lady beetles (Coleoptera: Coccinellidae), including Hippodamia convergens, Harmonia axyridis, Propylea quatrodecimpunctata, and Hippodamia variegata
6. Identifying and understanding the evolutionary history in regions of modern human genomes that are of “archaic” (e.g. Neanderthal) ancestry
Current “Dry” Lab Projects (Software Development/Testing)
7. Testing of PPP – the Pop-Gen Pipeline Platform, developing Jupyter Notebooks on publicly available RADseq datasets (Python)
8. Development, deployment, testing of a PPP GUI via The Galaxy Project (usegalaxy.org) (Python/XML)
9. Testing p-MULTICLUST, a parallelized method for estimating population structure (C, Python)
10. Developing a new software for estimating genetic relatedness (C/C++/Python)
Come join us!
Andrew recently presented his Summer research describing the assembly and annotation of the convergent lady beetle (Hippodamia convergens) genome, and phylogenomic history of Coleoptera at the CSUSM Summer Research Symposium. Congrats, Andrew! We are so proud of his accomplishments in such a small period of time, and wish him the best as he heads back to IU Bloomington!