Nicolás Mongiardino Koch
@phyloprog
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Postdoc @Scripps_Ocean . Deep-time evolutionary biology, from genomes to fossils. If it's not a phylogeny, I don't care 🇦🇷
San Diego, CA
Joined October 2018
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Pinned Tweet
I am extremely happy to share with all of you that I have accepted a position as Assistant Professor of Phylogenetics at Colorado State University 1/6
@ColoradoStateU
@csubiology
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If you ever wondered how much universities pay assistant professors, and how that compares to the local cost of living, wonder no more..
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No, of course I haven't spent two full days making this figure. Why would you even ask?
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Not often you encounter a phylum for the first time while on a hike. Take that birding
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There are species that are hard to love, and then there's Pseudostichopus sea cucumbers
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Beautiful siphonophore seen today at ~500 m on our way to the bottom
@SchmidtOcean
#BiodiverseSCB
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Yes they are generally called dinosaurs
is there a name for species known/described from only 1 specimen? and/or is there a list of how common that is?
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The people have asked for a color-blind scheme, better labelling, and access to data.
The people shall receive what they want (except for appropriate salaries)
Link to data:
If you ever wondered how much universities pay assistant professors, and how that compares to the local cost of living, wonder no more..
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I am thrilled to share that
@NSF
has funded our project to explore the evolutionary history of sea urchins by combining genomics with the fossil record!!
To this end, I’ll soon be joining Greg Rouse’s lab at
@Scripps_Ocean
as a postdoc
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Frustrated because
#phylogenomic
runs are taking months? Curious to see if results are driven by misleading loci?
Phylogenomic datasets are sometimes too big and complex for their own good. Here is a guide on how to find smaller sets of reliable genes!🧬
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Yesterday I thought this lockdown couldn’t get more boring.
Today my wife and I delivered our son in the entrance hallway of a hospital, joined only by a panicking security guard screaming for help.
Welcome son.
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Nearly 30 years ago, Sam Ciurca found a strange fossil amidst Silurian eurypterids in Ontario. He called it "the most beautiful fossil ever found", yet had no idea what it was
Today we describe it and put forward a hypothesis
@CurrentBiology
@yalepeabody
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I'm really happy to share my views on this topic, since I worked on it throughout the pandemic and never got to present it anywhere
So if you are inferring trees and have too many genes, or are wondering whether some of them are really that useful, see you on Nov 18th
Save the date and spread the word!
The next "Breaking Isolation", virtual lectures hosted the Willi Hennig Society, will be held on the 18th of November.
This time, we are having awesome lectures by
@zosterophyllum
and
@phyloprog
Follow the link in the description to join!
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This is a pretty special one: it’s my 30th paper!! 😊
Now can I please get a job?
Simulations show that timescaling of phylogenies is not severely hampered by inaccuracies in placement of fossils on the tree of life
@phyloprog
@RussellGarwood
@Cambriannelids
@wileyearthspace
@PaleoDB
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Seen today in the lab: Beautiful Chaetopterus (parchment) worms removed from their tubes
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I received tissue samples from ~30 species, most of which are from the deep sea. I wonder how much money it cost to gather these. The value held by museums is insane
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My biggest regret as a scientist is working on a clade for which silhouettes aren’t very informative
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Ok, I let the good news run free for a couple of weeks, but now it is time for episode two of this story. One detail that I left out of my original post is the starting date of my appointment, which will be August 2026 1/10
I am extremely happy to share with all of you that I have accepted a position as Assistant Professor of Phylogenetics at Colorado State University 1/6
@ColoradoStateU
@csubiology
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Sea urchins are so 2010s, so I present to you the first phylogenomic study of sea cucumbers
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Fossils improve phylogenetic analyses of morphological characters
That’s it. That’s the tweet.
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I got to spend valentines day in the wonderful company of some pencil sea urchins
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I am really happy to share a preprint that
@millacarmonia
and I just released, including our new R package chronospace, which includes novel tools to explore and visualize sensitivity in the estimation of divergence times 1/x
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New time-calibrated, genome-scale phylogeny of sea urchins just dropped on
@eLife
, with
@echinerd
,
@faguilgen
,
@hatch_sea
and many others!
I'm extremely happy to see this last PhD thesis chapter published!! 🥳
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@AndrewBarnas
Whenever I see people citing me incorrectly I wonder how many times I’ve done it myself 🤔
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New paper alert! "Chronogram or phylogram for ancestral state estimation? Model-fit statistics indicate the branch lengths underlying a binary character’s evolution" with
@Jeremy_spiders
and Martín Ramírez is now out in
@MethodsEcolEvol
A thread 👇
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Yesterday I submitted my PhD thesis!
The last edit was enlarging a figure to add one more page to it because what respectable human being sends out a thesis with a number of pages finishing in 49
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Yesterday I defended my PhD dissertation! Thanks to all of you who showed up, it meant a lot
While all of the science in my thesis is already online, there is one page that can't be found anywhere, and yet is the one that deserves to be shared the most
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I received whaaat?? 🤯
Made a brief stop from unpacking boxes in our new home to see this.
Thanks to whoever considered our work with
@Cambriannelids
deserved this award!
I’m left speechless. I still remember being an undergrad dreaming about one day publishing at
@systbiol
Congrats to
@mpiresbr2
and
@phyloprog
for receiving the Publisher's Award for Excellence in Systematic Research
@systbiol
#evol2021
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I don’t know what I was expecting to find when I checked this jar in the lab, but giant antarctic nemertean was definitely not a top guess
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Phylogenomics of sea cucumbers with
@TilicEkin
,
@RubySeadragon
, and others is out today in Proc B!
@RSocPublishing
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I will never agree with the existence of this urchin
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Very happy for this opportunity to share my research on sand dollars!
Join us Thursday at 4pm for "How Nature Innovates: The Origins of Sand Dollars"
@Yale
's Nicolás Mongiardino Koch traces the evolutionary history of these unique creatures to demonstrate how new groups of organisms arise.
Register here:
@phyloprog
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Sea urchins do not get big, but some get REALLY small. Here is the smallest living species of micro-echinoid, Fibularia nutriens. Female specimens (which are bigger than males) reach body lengths of only about 4.5 mm
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@eva_karasmanis
My rent at UCSD staff housing + after-school program for kid
#1
+ daycare for kid
#2
= 100.7% of my postdoc salary 😖
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My latest paper on phylogenomic subsampling is out now in
@MolBioEvol
! It describes a novel approach to sort and prioritize loci that relies on a multivariate analysis of gene properties to discover genes with high signal and low biases 1/8
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Interested in modeling the evolution of traits across macroevolutionary adaptive landscapes?
I have made available some R functions that extend current methods to infer multi-OU models (). 1/5
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Cluster support person: "This is a 100-day job, which is not common in the HPC"
Me: "Son, let me tell you about the time I ran Phylobayes for 7 months and it didn't converge"
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I spent all of yesterday coding this lineage-through-time plot by optimized state from stochastic character mappings and so I am forced to share it
😍 the superiority of paleo LTTs!
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To think that 7 years ago she was already copy editing my work
Pro tip: teach your kid Photoshop and they’ll become highly committed figure editors 👌
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well that only took (checks runtimes)... 25 days to converge
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Oh hell yeah! We made it to the top five most-cited papers in Proceedings B 🏆
@Cambriannelids
@RussellGarwood
you owe so many beers
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There is nothing that takes the edge off the job season like working on completely random stuff. So today I bring to you deWoRMR, an R script for web scraping taxonomic information from the World Register of Marine Species
@WRMarineSpecies
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Pro tip: teach your kid Photoshop and they’ll become highly committed figure editors 👌
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As of today I have reviewed more manuscripts than the ones I’ve authored.
I am officially…
a reviewer
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Official first day as postdoc at
@Scripps_Ocean
… which I’ll be spending home because daycare is closed
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In a new edition of “papers you don’t need to read because the title says it all”,
@Cambriannelids
,
@RussellGarwood
and myself present:
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Stalked glass sponge sitting 2 meters above the sea floor at Little Joe seamount
@SchmidtOcean
#BiodiverseSCB
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I took average asst prof salaries from and annual cost of living from (both in k of $), and matched them at the county level. I used the estimated budget for a family of 4, and filtered the data to only public R1 institutions
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Very excited to share with you my most recent work and last chapter of my PhD dissertation: "Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record" (1/n)
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Our paper on sea urchin phylogenomics is finally out! A thorough analysis of new transcriptomic data suggests major changes to our understanding of their evolutionary relationships.
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So.. what will I do for the next couple of years?? I have some ideas, which I'll share in episode 3 of this saga, but the list will definitely include joining my friends in the fight to defend science and the people that make it happen 10/10
Massive protests today all over Argentina as the president tries to pass a bill to accumulate legislative powers, sharply deregulate economic and environmental laws, and slash funding for science, culture, education, and everything we love
La patria no se vende
CONICET en lucha
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"Exploring adaptive landscapes across deep time: A case study using echinoid body size"
A solo endeavor out today in
@journal_evo
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How and why do
#fossils
affect phylogenies?
What can morphological data contribute in the genomic era?
This and more from
@Cambriannelids
and myself here:
Likely (untestable) the first
@systbiol
paper with a metal reference in the title!
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Sorry to miss
#Evol2022
again this year, but there was another trip that has also been delayed 3 years that had to happen
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Embrace it
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My daughter calls the asterisk “sea urchin”. I think this should be a thing
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Preprint alert!
"Fossils improve phylogenetic analyses of morphological characters" by myself,
@RussellGarwood
and
@Cambriannelids
, a team united by a shared love for phylogenies, fossils, and heavy metal.
TL;DR
Fossils -> GOOD ✅
Tip-dating -> GOOD ✅
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Auspicious start to our cruise as a rainbow blesses the R/V Falkor on our boarding day
@SchmidtOcean
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Luca and I are grateful for the opportunity to listen to exciting research and participate from such a cool conference!
@SBEmeeting
Tune in tomorrow for my talk on sea urchin phylogenomics and the fossil record. Livestream:
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I noticed that all my social media pics showcase my older daughter, so it was time to reduce the bias with a new profile pic
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Places in green are above the 1:1 line, so they pay asst profs enough to maintain a 4 people family (pretty neat 👌). Those in yellow don't, but they still pay above average (lin reg). In red are those that, relative to local cost of life, underpay compared to peer institutions
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Should ancestral state reconstructions in echinoderms be shown as pentagonal pie charts??
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Making the supplementary figures for this has been really fun... did the K-Pg trigger a rapid diversification of weevils? It depends on which genes you choose
I am really happy to share a preprint that
@millacarmonia
and I just released, including our new R package chronospace, which includes novel tools to explore and visualize sensitivity in the estimation of divergence times 1/x
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Divergence times for a metazoan phylum estimated using skyline FBD models.
Interpretation A: we can accurately estimate ancient divergence times from small morphological datasets.
Interpretation B: we cannot estimate ancient divergence times regardless of data type or size.
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Today’s tide pool highlight is Navanax inermis, a really pretty headshield slug
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Continuing with the awards, today we have Echinocrepis rostrata, a top contender for the most weirdly shaped urchin!
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Today was the last class of my Intro to R course and one of my students baked me a cinnamon sourdough and thanked me for a wonderful quarter 🥲
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Only 2 weeks to PhD defense!!
If anyone wants to come just send me a DM and I’ll share the link 🙂
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Extremely excited about this opportunity!! Morphological phylogenetics is more exciting than ever, and it's wonderful to get a chance to share this with others
There's a few more spots if you know of anyone that would be interested!
We have a new instructor! The amazing
@phyloprog
(Nicholas Mongiardino Koch) will be joining me in teaching the morphological phylogenetics workshop with
@TransmitScience
!!
We still have spots open. Please share to anyone interested!
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Very excited for tomorrow.. Genomes, fossils, echinoids!
Only 2 weeks to PhD defense!!
If anyone wants to come just send me a DM and I’ll share the link 🙂
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The nested patterns of symmetry in a brittle star are mind blowing
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Very excited to share this thing
@echinerd
and I did!!
Phylogenomics, morphology, fossils, time-calibration, macroevolution, adaptive landscapes, a new method for subsampling molecular datasets, a revised phylogeny of echinoids, and more..
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Cukes are insane. They can be just a few mm or 5 m long. They can live buried, attached to rocks, or even swimming. And they have deviated from the basic echinoderm organization, becoming worm-like, and in many cases losing their skeleton and even their tube feet. Look at them 🤩
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My 5yo saw a seagull, got all excited because she realized the feet were like those of ducks, and concluded they must be the same thing and she will start calling them ducks.
#lumper
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"Unexpectedly metal" is now my favorite compliment
@Cambriannelids
stumbled upon unexpectedly metal paper title
Nicolás Mongiardino Koch, Luke A Parry (2020). "Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses," Systematic Biology.
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And today’s prize for the prettiest colors goes to this diadematid urchin from Chile 🏅
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It is a huge honor to be giving this talk!
If you are interested consider attending
#SBEmeeting2020
, an online conference with an amazing line-up of talks on phylogenetics, evolution and paleontology. Registration is free!
We're very excited to have
@phyloprog
as our keynote speaker in the 𝑺𝒚𝒎𝒑𝒐𝒔𝒊𝒖𝒎 𝒐𝒇 𝑷𝒂𝒍𝒆𝒐𝒏𝒕𝒐𝒍𝒐𝒈𝒚 𝒂𝒏𝒅 𝑷𝒉𝒚𝒍𝒐𝒈𝒆𝒏𝒆𝒕𝒊𝒄𝒔!
#SBEmeeting2020
His research lies in the intersection of phylogenomics and phylogenetic paleobiology, focusing on echinoids.
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A reminder that living spiders, ray-finned fishes and seed plants originated more or less at the same time 👍😯
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I feel like every vert paleo tree these days is rooted in Euparkeria. We should just formalize it as a member of the family Outgroupidae
Being a phylo-dweeb I was interested in the phylogenetic analysis. The paper presents this solution, but I can't find any explanation how in the text or SI i.e. type of analysis, software, settings etc. Fig 22 3/n
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I have made this method for mining useful genes from phylogenomic datasets available as an R script. Check it out at and let me know if you find any bugs 🙏
Frustrated because
#phylogenomic
runs are taking months? Curious to see if results are driven by misleading loci?
Phylogenomic datasets are sometimes too big and complex for their own good. Here is a guide on how to find smaller sets of reliable genes!🧬
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Imagine one of these entering the fossil record
Monocephalic conjoined scorpions exist - and they look like bizarre alchemical symbols come to life!
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First time having a dishwasher in my life. I love it, really handy
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In a couple of weeks I'll have the amazing opportunity to board
@SchmidtOcean
's R/V Falkor and explore the biodiversity of the Pacific depths off the coast of California. Or as I explained it to my daughter, I will begin my Octonaut training.
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Desk shrinkage, a little known side effect of moving out
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Very excited to share a preprint of this project with
@Cambriannelids
Fossils impact topology more than extant taxa and rearrange trees in entirely unique ways.
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4 years ago
@dsmithparedes
and I had all World Cup matches playing on the tv in our office
@Yale
and people would just come, sit down and watch with us.
Trying to keep the tradition alive
@Scripps_Ocean
. We’ll see who comes
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Homeschooling is going great, we are covering all the basics
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