@smishra677.bsky.social
PhD student at Hahn Lab IUB. --working on developing algorithms for problems in phylogenetic and population genetics
Interest includes #MUFC
Interest includes #MUFC
Reposted
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 11:10 AM
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
Reposted
Also, if you don't want to bother to read the preprint, you can just watch my talk on these results from this past year's Evolution meeting:
2/2
bsky.app/profile/3rdr...
2/2
bsky.app/profile/3rdr...
Here is a video of my talk for those interested:
www.youtube.com/watch?v=GmcU...
www.youtube.com/watch?v=GmcU...
February 6, 2025 at 4:30 PM
Also, if you don't want to bother to read the preprint, you can just watch my talk on these results from this past year's Evolution meeting:
2/2
bsky.app/profile/3rdr...
2/2
bsky.app/profile/3rdr...
Reposted
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
January 8, 2026 at 1:57 PM
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
Reposted
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting
Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizont...
www.biorxiv.org
January 7, 2026 at 11:22 AM
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
Reposted
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
No molecular evidence for Muller's ratchet in mitochondrial genomes
Muller's ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mi...
www.biorxiv.org
December 17, 2025 at 2:36 PM
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Reposted
No molecular evidence for Muller's ratchet in mitochondrial genomes https://www.biorxiv.org/content/10.64898/2025.12.16.694700v1
December 17, 2025 at 3:33 AM
No molecular evidence for Muller's ratchet in mitochondrial genomes https://www.biorxiv.org/content/10.64898/2025.12.16.694700v1
Reposted
New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance
1/
www.biorxiv.org/content/10.1...
1/
www.biorxiv.org/content/10.1...
Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees
Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories...
www.biorxiv.org
October 7, 2025 at 3:10 PM
New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance
1/
www.biorxiv.org/content/10.1...
1/
www.biorxiv.org/content/10.1...
Reposted
Happy that our new paper is out, led by super-postbacc Daniel Rickert (now a PhD student at UNC). Also kind of excited to have my first TPB paper...
1/2
"Inconsistency of parsimony under the multispecies coalescent"
www.sciencedirect.com/science/arti...
1/2
"Inconsistency of parsimony under the multispecies coalescent"
www.sciencedirect.com/science/arti...
Inconsistency of parsimony under the multispecies coalescent
While it is known that parsimony can be statistically inconsistent under certain models of evolution due to high levels of homoplasy, the consistency …
www.sciencedirect.com
September 30, 2025 at 2:06 PM
Happy that our new paper is out, led by super-postbacc Daniel Rickert (now a PhD student at UNC). Also kind of excited to have my first TPB paper...
1/2
"Inconsistency of parsimony under the multispecies coalescent"
www.sciencedirect.com/science/arti...
1/2
"Inconsistency of parsimony under the multispecies coalescent"
www.sciencedirect.com/science/arti...
Reposted
New paper led by @yadirapga.bsky.social!
Opossums have babies at 6-months of age, but are still highly male-biased in their mutations
academic.oup.com/genetics/adv...
Opossums have babies at 6-months of age, but are still highly male-biased in their mutations
academic.oup.com/genetics/adv...
Low mutation rate but high male-bias in the germline of a short-lived opossum
Abstract. Age and sex have been found to be important determinants of the mutation rate per generation in mammals, but the mechanisms underlying these fact
academic.oup.com
September 1, 2025 at 7:09 PM
New paper led by @yadirapga.bsky.social!
Opossums have babies at 6-months of age, but are still highly male-biased in their mutations
academic.oup.com/genetics/adv...
Opossums have babies at 6-months of age, but are still highly male-biased in their mutations
academic.oup.com/genetics/adv...
Reposted
In #GENETICS, @3rdreviewer.bsky.social and @smishra677.bsky.social show it is possible to estimate recombination solely using the allele frequency spectrum and provide a genealogical interpretation of the results, showing how #MachineLearning can provide insights into biology.
buff.ly/emixz9W
buff.ly/emixz9W
July 16, 2025 at 10:04 PM
In #GENETICS, @3rdreviewer.bsky.social and @smishra677.bsky.social show it is possible to estimate recombination solely using the allele frequency spectrum and provide a genealogical interpretation of the results, showing how #MachineLearning can provide insights into biology.
buff.ly/emixz9W
buff.ly/emixz9W
Reposted
June 6, 2025 at 6:33 PM
Reposted
New paper with Sarthak Mishra! Maybe it will bring you some joy given all this (waves arms around).
"Estimating recombination using only the allele frequency spectrum"
1/2
www.biorxiv.org/content/10.1...
"Estimating recombination using only the allele frequency spectrum"
1/2
www.biorxiv.org/content/10.1...
Estimating recombination using only the allele frequency spectrum
Standard methods for estimating the population recombination parameter, rho, are dependent on sampling individual genotypes and calculating various types of disequilibria. However, recent machine lear...
www.biorxiv.org
February 6, 2025 at 4:29 PM
New paper with Sarthak Mishra! Maybe it will bring you some joy given all this (waves arms around).
"Estimating recombination using only the allele frequency spectrum"
1/2
www.biorxiv.org/content/10.1...
"Estimating recombination using only the allele frequency spectrum"
1/2
www.biorxiv.org/content/10.1...