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Pankaj Dhakad

@pankajd.bsky.social
78 followers 129 following 1 posts

Postdoc at UC Davis Bioinformatics | Evolutionary genetics | Molecular evolution

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Reposted by Pankaj Dhakad
Genome Biology and Evolution @genomebiolevol.bsky.social · 09/03/2026
@pankajd.bsky.social & @darrenobbard.bsky.social show that immune genes overall evolve faster at the protein level, but are less prone to copy-number changes than other genes in Drosophila. 🔗 doi.org/10.1093/gbe/evag034 #genome #evolution #drosophila
doi.org
Predictors of Protein Evolution in the drosophilid Immune System
Abstract. The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional spec
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Reposted by Pankaj Dhakad
Ben Hopkins @brhopkins92.bsky.social · 06/03/2026
Quick plug for our new resource, the Drosophila Species Stock Exchange. This is a database and mailing list that documents species currently in culture and the labs holding them. If you want to know more or sign up then please get in touch. See attached for more info and please share!
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Reposted by Pankaj Dhakad
Mark A. Hanson @hansonmark.bsky.social · 06/03/2026
Pleased to finally share this fun collab that began at #Ento23 @cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun). Horizontal transfer of an #AntimicrobialPeptide across insects bit.ly/DrsHGT 1/🧵
A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insectsVarious phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genesAntimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of
horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the
distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired
pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT
events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.
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Reposted by Pankaj Dhakad
fly paper broadcast @fly-broadcast.bsky.social · 05/03/2026
The role of haltere campaniform sensilla on equilibrium reflexes of the fruit fly, Drosophila melanogaster #Drosophila
pubmed.ncbi.nlm.nih.gov
The role of haltere campaniform sensilla on equilibrium reflexes of the fruit fly, Drosophila melanogaster #Drosophila
PubMed link
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Pankaj Dhakad @pankajd.bsky.social · 20/02/2026
Predictors of protein evolution in the drosophilid immune system url: academic.oup.com/gbe/article/... #Drosohila #Immunity #fly #Evolution #Geneturnover #AdaptiveEvolution #Predictors #OrthologousGeneFamilies
academic.oup.com
Predictors of protein evolution in the drosophilid immune system
Abstract. The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional spec
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Reposted by Pankaj Dhakad
Dmitri Petrov @petrovadmitri.bsky.social · 19/02/2026
The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io
bapg-conference.github.io
BAPG Spring 2026
Bay Area Population Genomics Conference
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Reposted by Pankaj Dhakad
PLOS Biology @plosbiology.org · 20/02/2026
The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI
Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.
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Reposted by Pankaj Dhakad
fly paper broadcast @fly-broadcast.bsky.social · 16/02/2026
Predictors of protein evolution in the drosophilid immune system #Drosophila
pubmed.ncbi.nlm.nih.gov
Predictors of protein evolution in the drosophilid immune system #Drosophila
PubMed link
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Reposted by Pankaj Dhakad
fly paper broadcast @fly-broadcast.bsky.social · 04/02/2026
Transcriptomic analysis of non-model Drosophilidae reveals novel AMP candidates #Drosophila
pubmed.ncbi.nlm.nih.gov
Transcriptomic analysis of non-model Drosophilidae reveals novel AMP candidates #Drosophila
PubMed link
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Reposted by Pankaj Dhakad
Darren Obbard @darrenobbard.bsky.social · 16/09/2025
Another preprint from @pankajd.bsky.social ! www.biorxiv.org/content/10.1...
biorxiv.org
Predictors of protein evolution in the drosophilid immune system
The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understoo...
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Reposted by Pankaj Dhakad
Darren Obbard @darrenobbard.bsky.social · 09/06/2025
Next paper from @pankajd.bsky.social ! www.biorxiv.org/content/10.1...
biorxiv.org
Transcriptomic analysis of non-model Drosophilidae reveals novel AMP candidates
Background Drosophila melanogaster has been a valuable model for dissecting the molecular architecture of innate immunity. However, the family Drosophilidae encompasses over 4000 species, spanning dee...
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