Martin R. Smith
@palaeosmith.bsky.social
Palaeontologist developing phylogenetic and stratigraphic methods to understand the origins of life's rich diversity
My new package Coreset is now on CRAN.
ms609.github.io/Coreset/
Use its MaxMin Diversity selector to obtain an unbiased and representative subsample of most parsimonious trees (paper forthcoming...)
ms609.github.io/Coreset/
Use its MaxMin Diversity selector to obtain an unbiased and representative subsample of most parsimonious trees (paper forthcoming...)
Discrete Diversity, Dispersion, and Coverage Subset Selection
Solves discrete location objectives on a distance matrix or Euclidean coordinate set. The Max-Min Diversity (MMDP / p-dispersion) objective, which maximizes the minimum pairwise distance within a sele...
ms609.github.io
September 24, 2026 at 12:45 PM
My new package Coreset is now on CRAN.
ms609.github.io/Coreset/
Use its MaxMin Diversity selector to obtain an unbiased and representative subsample of most parsimonious trees (paper forthcoming...)
ms609.github.io/Coreset/
Use its MaxMin Diversity selector to obtain an unbiased and representative subsample of most parsimonious trees (paper forthcoming...)
Hemichordate gills weren't made for breathing: vertebrates pioneered the use of gills for gas exchange
journals.biologists.com/jeb/article/...
journals.biologists.com/jeb/article/...
Gills are not the primary site of gas exchange in the suspension-feeding hemichordate Protoglossus graveolens
Highlighted Article: New functional data from hemichordates provide critical support for a vertebrate origin of gas exchange at gills.
journals.biologists.com
September 17, 2026 at 9:33 AM
Hemichordate gills weren't made for breathing: vertebrates pioneered the use of gills for gas exchange
journals.biologists.com/jeb/article/...
journals.biologists.com/jeb/article/...
Fast and innovative methods for building consensus trees: package ConsTree is now on CRAN
constree.github.io
constree.github.io
ConsTree: Fast Algorithms for Phylogenetic Consensus Trees
Efficient construction of phylogenetic consensus trees. Methods include strict, majority-rule, majority-rule (+), loose (combinable component / semi-strict), greedy, Adams, frequency difference, R*, a...
cran.r-project.org
September 15, 2026 at 12:27 PM
Fast and innovative methods for building consensus trees: package ConsTree is now on CRAN
constree.github.io
constree.github.io
Ever wondered which characters support individual clades in a tree? My new method maps phylogenetic support across a dataset.
doi.org/10.1093/sysb...
Try it in R:
pak::pkg_install("ms609/TreeSearch@cpp-search")
?TreeSearch::ClusteringConcordance
doi.org/10.1093/sysb...
Try it in R:
pak::pkg_install("ms609/TreeSearch@cpp-search")
?TreeSearch::ClusteringConcordance
September 14, 2026 at 9:56 AM
Ever wondered which characters support individual clades in a tree? My new method maps phylogenetic support across a dataset.
doi.org/10.1093/sysb...
Try it in R:
pak::pkg_install("ms609/TreeSearch@cpp-search")
?TreeSearch::ClusteringConcordance
doi.org/10.1093/sysb...
Try it in R:
pak::pkg_install("ms609/TreeSearch@cpp-search")
?TreeSearch::ClusteringConcordance
Tree space mapping made easy:
Map landscapes of phylogenetic trees in TreeDist without installing R! ms609.github.io/TreeDist/app/
(Allow a minute for the app to load.)
Map landscapes of phylogenetic trees in TreeDist without installing R! ms609.github.io/TreeDist/app/
(Allow a minute for the app to load.)
Shiny App
ms609.github.io
September 4, 2026 at 12:39 PM
Tree space mapping made easy:
Map landscapes of phylogenetic trees in TreeDist without installing R! ms609.github.io/TreeDist/app/
(Allow a minute for the app to load.)
Map landscapes of phylogenetic trees in TreeDist without installing R! ms609.github.io/TreeDist/app/
(Allow a minute for the app to load.)
It's easier to lose a morphological trait than to gain one.
When models and datasets reflect this asymmetry, phylogenetic reconstructions improve.
doi.org/10.1093/sysb...
When models and datasets reflect this asymmetry, phylogenetic reconstructions improve.
doi.org/10.1093/sysb...
August 18, 2026 at 8:10 AM
It's easier to lose a morphological trait than to gain one.
When models and datasets reflect this asymmetry, phylogenetic reconstructions improve.
doi.org/10.1093/sysb...
When models and datasets reflect this asymmetry, phylogenetic reconstructions improve.
doi.org/10.1093/sysb...
Burgess Shale-type preservation of Ediacaran Fronds
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The terminal Ediacaran Tongshan Lagerstätte from South China - Nature Communications
Here, the authors present Ediacaran fossils from the Tongshan Lagerstätte (South China), including Burgess Shale-type rangeomorphs preserved both with fronds and holdfasts. They use sedimentary and ch...
www.nature.com
November 24, 2025 at 9:47 AM
Burgess Shale-type preservation of Ediacaran Fronds
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Chromosomes point to Lophophorate monophyly
www.cell.com/current-biol...
I wonder what this topology means for the origins of Bryozoans?
www.cell.com/current-biol...
I wonder what this topology means for the origins of Bryozoans?
Phoronid genome supports a monophyletic Lophophorata
The definition and membership of Lophophorata, including brachiopods, phoronids, and
bryozoans, have been debated for over a century. Lewin et al. show that phoronids
and bryozoans share multiple deri...
www.cell.com
November 10, 2025 at 3:54 PM
Chromosomes point to Lophophorate monophyly
www.cell.com/current-biol...
I wonder what this topology means for the origins of Bryozoans?
www.cell.com/current-biol...
I wonder what this topology means for the origins of Bryozoans?
There were at least five independent origins of lichens – and at least one had occurred by the Devonian
www.science.org/doi/pdf/10.1...
www.science.org/doi/pdf/10.1...
November 3, 2025 at 6:55 AM
There were at least five independent origins of lichens – and at least one had occurred by the Devonian
www.science.org/doi/pdf/10.1...
www.science.org/doi/pdf/10.1...
Is the anus a gonopore? Origins of the bilaterian through-gut
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular evidence from xenacoelomorph gonopore formation supports homology with the bilaterian anus - Nature Ecology & Evolution
The evolutionary origin of the bilaterian gut with two openings is debated. Expression in xenacoelomorphs, the sister group to bilaterians, of genes involved in bilaterian gut patterning suggests that...
www.nature.com
October 28, 2025 at 5:16 AM
Is the anus a gonopore? Origins of the bilaterian through-gut
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Martin R. Smith
Our new paper is out: StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling doi.org/10.5194/gchr... with @palaeosmith.bsky.social Kilian Eichenseer & Matthias Sinnesael
StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling
Abstract. Stratigraphic correlation and age modelling are fundamental to reconstructing Earth's history, biological evolution, and palaeoclimate, and underpin the exploration for subsurface resources....
doi.org
October 27, 2025 at 9:26 AM
Our new paper is out: StratoBayes: a Bayesian method for automated stratigraphic correlation and age modelling doi.org/10.5194/gchr... with @palaeosmith.bsky.social Kilian Eichenseer & Matthias Sinnesael
Have we reached 'peak fossil'?
Sampling bias hardly affects the lizard fossil record – suggesting that new finds are unlikely to overhaul our understanding?
doi.org/10.1017/pab....
Sampling bias hardly affects the lizard fossil record – suggesting that new finds are unlikely to overhaul our understanding?
doi.org/10.1017/pab....
Taphonomic megabiases constrain phylogenetic information in the squamate fossil record | Paleobiology | Cambridge Core
Taphonomic megabiases constrain phylogenetic information in the squamate fossil record
doi.org
September 29, 2025 at 8:54 AM
Have we reached 'peak fossil'?
Sampling bias hardly affects the lizard fossil record – suggesting that new finds are unlikely to overhaul our understanding?
doi.org/10.1017/pab....
Sampling bias hardly affects the lizard fossil record – suggesting that new finds are unlikely to overhaul our understanding?
doi.org/10.1017/pab....
Fossil mushrooms from the Cretaceous – almost fresh enough to top a pizza with!
doi.org/10.1093/botl...
doi.org/10.1093/botl...
September 15, 2025 at 9:23 AM
Fossil mushrooms from the Cretaceous – almost fresh enough to top a pizza with!
doi.org/10.1093/botl...
doi.org/10.1093/botl...
What was burning? Evidence of Ediacaran wildfires doi.org/10.1016/j.gl...
June 20, 2025 at 8:52 AM
What was burning? Evidence of Ediacaran wildfires doi.org/10.1016/j.gl...
An early "mollusc" reconsidered: Is Shishana, in fact, a chancelloriid?
Read our new paper @science.org
www.science.org/doi/10.1126/...
Read our new paper @science.org
www.science.org/doi/10.1126/...
May 9, 2025 at 6:36 AM
An early "mollusc" reconsidered: Is Shishana, in fact, a chancelloriid?
Read our new paper @science.org
www.science.org/doi/10.1126/...
Read our new paper @science.org
www.science.org/doi/10.1126/...
StratoBayes: our quantitative tool for automated stratigraphic correlation.
Read the preprint: egusphere.copernicus.org/preprints/20...
Read the preprint: egusphere.copernicus.org/preprints/20...
April 4, 2025 at 9:32 AM
StratoBayes: our quantitative tool for automated stratigraphic correlation.
Read the preprint: egusphere.copernicus.org/preprints/20...
Read the preprint: egusphere.copernicus.org/preprints/20...
Is a borrowed bacterial gene key to the origins of biomineralization in animals?
academic.oup.com/gbe/article/...
academic.oup.com/gbe/article/...
Horizontal Transfer of msp130 Genes and the Evolution of Metazoan Biocalcification
Abstract. The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins o
academic.oup.com
March 3, 2025 at 9:57 AM
Is a borrowed bacterial gene key to the origins of biomineralization in animals?
academic.oup.com/gbe/article/...
academic.oup.com/gbe/article/...
Origin of the anus: was a gonopore key to inventing the through gut?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
February 17, 2025 at 12:11 PM
Origin of the anus: was a gonopore key to inventing the through gut?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Derived Cirratuliform annelids in Cambrian SCF deposits – possible relatives of Iotuba? onlinelibrary.wiley.com/doi/10.1111/...
February 6, 2025 at 11:15 AM
Derived Cirratuliform annelids in Cambrian SCF deposits – possible relatives of Iotuba? onlinelibrary.wiley.com/doi/10.1111/...
A Cambrian arms race?
www.cell.com/current-biol...
www.cell.com/current-biol...
Adaptive responses in Cambrian predator and prey highlight the arms race during the rise of animals
Bicknell et al. explore the hypothesis that predation was a major ecological driver of early animal evolution. A study of the early Cambrian tommotiid Lapworthella fasciculata shows a correlation between increasing shell thickness and predation intensity (evidenced by perforations) over time, representing the oldest known microevolutionary arms race.
www.cell.com
January 6, 2025 at 9:53 AM
A Cambrian arms race?
www.cell.com/current-biol...
www.cell.com/current-biol...
Burial not required for exceptional fossilization?
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Kaolinite induces rapid authigenic mineralisation in unburied shrimps - Communications Earth & Environment
Instantaneous burial capturing animals alive may not be prerequisite for exceptional marine animal preservation and fossilization, according to experiments on marine and freshwater shrimps and cryogen...
www.nature.com
January 6, 2025 at 9:49 AM
Burial not required for exceptional fossilization?
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Low but dynamic oxygen levels as the backdrop to the Cambrian radiation
www.research.ed.ac.uk/en/publicati...
www.research.ed.ac.uk/en/publicati...
Low oxygen but dynamic marine redox conditions permitted the Cambrian Radiation
www.research.ed.ac.uk
December 20, 2024 at 12:36 PM
Low but dynamic oxygen levels as the backdrop to the Cambrian radiation
www.research.ed.ac.uk/en/publicati...
www.research.ed.ac.uk/en/publicati...
Reposted by Martin R. Smith
🚨Job Alert!🚨
We are recruiting an Associate Professor in Environmental Sustainability! The post is associated with a new MSc in Environmental Sustainability which is due to start in October 2026. Please apply by 31 January, and please share this with your networks!
durham.taleo.net/careersectio...
We are recruiting an Associate Professor in Environmental Sustainability! The post is associated with a new MSc in Environmental Sustainability which is due to start in October 2026. Please apply by 31 January, and please share this with your networks!
durham.taleo.net/careersectio...
Associate Professor in Environmental Sustainability (EARTH_01)
Click the link provided to see the complete job description.
durham.taleo.net
December 4, 2024 at 3:34 PM
🚨Job Alert!🚨
We are recruiting an Associate Professor in Environmental Sustainability! The post is associated with a new MSc in Environmental Sustainability which is due to start in October 2026. Please apply by 31 January, and please share this with your networks!
durham.taleo.net/careersectio...
We are recruiting an Associate Professor in Environmental Sustainability! The post is associated with a new MSc in Environmental Sustainability which is due to start in October 2026. Please apply by 31 January, and please share this with your networks!
durham.taleo.net/careersectio...
Apply now for two PhD projects modelling stratigraphy to understand the evolutionary past and geological future
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...
Computational innovation for the energy transition: Bayesian stratigraphic correlation of subsurface data
iapetus2.ac.uk
November 20, 2024 at 11:59 AM
Apply now for two PhD projects modelling stratigraphy to understand the evolutionary past and geological future
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...
iapetus2.ac.uk/studentships...