This document discusses methods for inferring ancestor-descendant relationships among fossil taxa using tip-dating phylogenetic analyses. It summarizes research applying Bayesian tip-dating and other methods to datasets involving trilobites, brachiopods, dinosaurs, and other fossil groups. The results generally support more instances of "budding", where new taxa arise within existing lineages, rather than "anagenesis", where taxa gradually transform over time. The analyses also find many earliest occurrences serving as ancestors to later occurrences of the same morphotaxa.
GSA 2016 Talk: Inferring Ancestor-Descendant Relationships in the Fossil Reco...David Bapst
Tip-dating and cal3 are new methods that allow us to quantitatively infer the placement of fossil morphotaxa in ancestor-descendant sequences in phylogenies.
Full abstract here:
https://gsa.confex.com/gsa/2016AM/webprogram/Paper277591.html
Convergent evolution of squid photophores and transcriptomesTodd Oakley
Slides describing research published in PNAS, and BMC Evolutionary Biology. We found that light producing photophores evolved separately in two distantly related squid. Surprisingly, overall gene expression is amazingly similar.
These presentation covers heredity, mendel's brief story, mendel's first experiment, and mendelian law of inheritance.I also included assessment. I hope that I can help you, as much as I was. :D <3
GSA 2016 Talk: Inferring Ancestor-Descendant Relationships in the Fossil Reco...David Bapst
Tip-dating and cal3 are new methods that allow us to quantitatively infer the placement of fossil morphotaxa in ancestor-descendant sequences in phylogenies.
Full abstract here:
https://gsa.confex.com/gsa/2016AM/webprogram/Paper277591.html
Convergent evolution of squid photophores and transcriptomesTodd Oakley
Slides describing research published in PNAS, and BMC Evolutionary Biology. We found that light producing photophores evolved separately in two distantly related squid. Surprisingly, overall gene expression is amazingly similar.
These presentation covers heredity, mendel's brief story, mendel's first experiment, and mendelian law of inheritance.I also included assessment. I hope that I can help you, as much as I was. :D <3
This presentation is carrying all summary about the history of genetics that who discover genes which scientist work on it and there work summary of all these things is given here and it is very helpful for the students of genetics whether they are students of plant genetics or animals.
On the Origin of Morphospecies: Using Bayesian Phylogenetics to Quantify the ...David Bapst
If a fossil record is well-sampled, first principles predict that there is then a reasonable expectation that some observed morpho-species might be ancestral to other taxa. Modern tip-dating Bayesian phylogenetics employ explicit models of sampling in the fossil record, thus providing a quantitative framework for estimating sampled ancestors. Furthermore, the processes by which new morphologically-distinguishable chrono-species arise can be distinguished by comparing estimated divergence times against the stratigraphic ranges of their inferred ancestors. Ancestor-descendant relationships are often categorized into three possible modes, with morphotaxa originating (1) via ‘anagenetic’ changes independent of branching, (2) by symmetrically ‘bifurcating’ into two new morphotaxa, or (3) by morphologically distinct descendants ‘budding’ off their morphologically-persistent ancestor. Specific cases have been attributed to each pattern, but there is little consensus on which mode is most common, or whether these dynamics vary across and within major fossil-rich groups. Our assumptions about the mode of ancestor-descendant relationships have broad impacts on our interpretation of evolutionary history, from whether we expect morphological change to correlate with speciation, or whether taxonomic turnover in the fossil record might be artificially inflated by the pseudo-extinction implicit to anagenesis and bifurcation. Here, we assemble morphological matrices and stratigraphic range data from more than thirty studies of various invertebrate groups with well-sampled fossil records, predominantly Paleozoic groups, such as brachiopods, graptolites, trilobites, crinoids and other echinoderms. These datasets differ not only in the particular clades assessed, but also the taxonomic resolution and sampling schema. Using tip-dating Bayesian analyses, we address the extent to which sampled ancestors are inferred to occur in these fossil records, as well as the degree to which these records provide support for particular modes of morphological differentiation among taxa.
Authors:
BAPST, David W., Geology & Geophysics, Texas A & M University, 3115 TAMU, College Station, TX 77843-3115, WRIGHT, David F., Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, COLE, Selina R., Paleontology and HOPKINS, Melanie J., Division of Paleontology (Invertebrates), American Museum of Natural History, Central Park West at 79th Street, New York, NY, MELCHIN, Michael, Dept. of Earth Sciences, St. Francis Xavier Univ, Antigonish, Canada, CONGREVE, Curtis R., Geosciences, The Pennsylvania State University, University Park, PA 16802, LAMSDELL, James C., Geology & Geog/, West Virginia University, 98 Beechurst Avenue, Brooks Hall, Morgantown, WV, MITCHELL, Charles E., Geology, University at Buffalo, SUNY, 126 Cooke Hall, Buffalo, NY, and CARLSON, Sandra J., Earth and Planetary Sciences, University of California, Davis, One Shields Ave, Davis, CA
Evolution 2012 Talk: When do we Lack Resolvable Clades?David Bapst
A talk presenting my work recently published in PLoS One, at the Evolution meeting in 2012, in Ottawa. Examples of morphological differentiation illustrated with colorful pictures of a group known to many.
You can find the published paper here, without the pocket monsters:
Bapst DW (2013) When Can Clades Be Potentially Resolved with
Morphology? PLoS ONE 8(4): e62312. doi:10.1371/journal.pone.0062312
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062312
Obviously all the Pokemon are copyright of Nintendo of America. But how useful pedagogically they were!
Why phelogyny has to be this way not other way aroundExaplain bas.pdffazalenterprises
Why phelogyny has to be this way not other way around?
Exaplain based on evidence of
-fossil record
-genetic evdence
-Blast search engine
-nervous system
-body structure or itera itera ori platy helminthes Nematoda Chid a an, ermata Chrdota Chino
Solution
Fossil record & Genetic evidence:
It has clearly observed the predicted order of trait appearance has been increasing as the actual
order of appearance of trait increases among a group of species. Therefore, according to “a
descent with modification of a trait i.e. derived from a common ancestor (a fossil species arose
from a common ancestor)” specifically changing over time. This change was observed in
phylogenetic tree of multicellular organisms (from porifera with no symmetry to bilateral
symmetric species) as “a linear hypothetical relationship between the predicted order of trait
appearance based on trait nesting and the actual order of appearance in the fossil record for a
number of traits among a group of species”.
Fossil species are different and they are transitional fossils as they often resemble and exhibit
both the groups of organisms. They often different in the DNA sequences when perform DNA
sequencing even though they look similar morphologically thereby paleontologists often classify
them as per their interspecific and intraspecific genetic variations (pan genes, core genes)
variations. Fossils are formed due to catastrophism and gradualism, their classification is based
on their body size, and body weight for example dinosaurs is the common ancestors of both birds
and reptiles. Thereby different paleontologists show different family trees for the same fossils.
Blast search engine
The above multicellular eukaryotic classification as per PSI-BLAST considerably along with
matrix -based alignments is used to reveal the amino acid substitution in every species for gene
expression similarity so that protein synthesis can be compared with every species in relation to
higher eukaryotes (chordates). PPSM (position specific scoring matrix) is widely used to get
either positive or negative results in relation to the substitution of the amino acids for protein
multiple sequences.
Delta Blast is more useful in detecting and is identifying “species proteins from lower
multicellular porifera species to annelids, arthropods, non-chordates & chordates” in which
amino acid or nucleotide sequences of the species, which are not closely related compared to the
PSI- BLAST. Some time PSI-Blast also enables to get possible information in identifying the
evolutionary nucleotide substituent’s in the species, which are not closely related.
Nervous system:
The three animal phyla that best represent stages in the evolution of the nervous system of
animals are animals belongs to primitive bilateria, Cnidaria and Ctenophora since these are often
referred as Epitheliozoa. These animals often diversified from primitive sponges where primitive
neuronal system has developed already. The nervous system present.
This presentation is carrying all summary about the history of genetics that who discover genes which scientist work on it and there work summary of all these things is given here and it is very helpful for the students of genetics whether they are students of plant genetics or animals.
On the Origin of Morphospecies: Using Bayesian Phylogenetics to Quantify the ...David Bapst
If a fossil record is well-sampled, first principles predict that there is then a reasonable expectation that some observed morpho-species might be ancestral to other taxa. Modern tip-dating Bayesian phylogenetics employ explicit models of sampling in the fossil record, thus providing a quantitative framework for estimating sampled ancestors. Furthermore, the processes by which new morphologically-distinguishable chrono-species arise can be distinguished by comparing estimated divergence times against the stratigraphic ranges of their inferred ancestors. Ancestor-descendant relationships are often categorized into three possible modes, with morphotaxa originating (1) via ‘anagenetic’ changes independent of branching, (2) by symmetrically ‘bifurcating’ into two new morphotaxa, or (3) by morphologically distinct descendants ‘budding’ off their morphologically-persistent ancestor. Specific cases have been attributed to each pattern, but there is little consensus on which mode is most common, or whether these dynamics vary across and within major fossil-rich groups. Our assumptions about the mode of ancestor-descendant relationships have broad impacts on our interpretation of evolutionary history, from whether we expect morphological change to correlate with speciation, or whether taxonomic turnover in the fossil record might be artificially inflated by the pseudo-extinction implicit to anagenesis and bifurcation. Here, we assemble morphological matrices and stratigraphic range data from more than thirty studies of various invertebrate groups with well-sampled fossil records, predominantly Paleozoic groups, such as brachiopods, graptolites, trilobites, crinoids and other echinoderms. These datasets differ not only in the particular clades assessed, but also the taxonomic resolution and sampling schema. Using tip-dating Bayesian analyses, we address the extent to which sampled ancestors are inferred to occur in these fossil records, as well as the degree to which these records provide support for particular modes of morphological differentiation among taxa.
Authors:
BAPST, David W., Geology & Geophysics, Texas A & M University, 3115 TAMU, College Station, TX 77843-3115, WRIGHT, David F., Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, COLE, Selina R., Paleontology and HOPKINS, Melanie J., Division of Paleontology (Invertebrates), American Museum of Natural History, Central Park West at 79th Street, New York, NY, MELCHIN, Michael, Dept. of Earth Sciences, St. Francis Xavier Univ, Antigonish, Canada, CONGREVE, Curtis R., Geosciences, The Pennsylvania State University, University Park, PA 16802, LAMSDELL, James C., Geology & Geog/, West Virginia University, 98 Beechurst Avenue, Brooks Hall, Morgantown, WV, MITCHELL, Charles E., Geology, University at Buffalo, SUNY, 126 Cooke Hall, Buffalo, NY, and CARLSON, Sandra J., Earth and Planetary Sciences, University of California, Davis, One Shields Ave, Davis, CA
Evolution 2012 Talk: When do we Lack Resolvable Clades?David Bapst
A talk presenting my work recently published in PLoS One, at the Evolution meeting in 2012, in Ottawa. Examples of morphological differentiation illustrated with colorful pictures of a group known to many.
You can find the published paper here, without the pocket monsters:
Bapst DW (2013) When Can Clades Be Potentially Resolved with
Morphology? PLoS ONE 8(4): e62312. doi:10.1371/journal.pone.0062312
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062312
Obviously all the Pokemon are copyright of Nintendo of America. But how useful pedagogically they were!
Why phelogyny has to be this way not other way aroundExaplain bas.pdffazalenterprises
Why phelogyny has to be this way not other way around?
Exaplain based on evidence of
-fossil record
-genetic evdence
-Blast search engine
-nervous system
-body structure or itera itera ori platy helminthes Nematoda Chid a an, ermata Chrdota Chino
Solution
Fossil record & Genetic evidence:
It has clearly observed the predicted order of trait appearance has been increasing as the actual
order of appearance of trait increases among a group of species. Therefore, according to “a
descent with modification of a trait i.e. derived from a common ancestor (a fossil species arose
from a common ancestor)” specifically changing over time. This change was observed in
phylogenetic tree of multicellular organisms (from porifera with no symmetry to bilateral
symmetric species) as “a linear hypothetical relationship between the predicted order of trait
appearance based on trait nesting and the actual order of appearance in the fossil record for a
number of traits among a group of species”.
Fossil species are different and they are transitional fossils as they often resemble and exhibit
both the groups of organisms. They often different in the DNA sequences when perform DNA
sequencing even though they look similar morphologically thereby paleontologists often classify
them as per their interspecific and intraspecific genetic variations (pan genes, core genes)
variations. Fossils are formed due to catastrophism and gradualism, their classification is based
on their body size, and body weight for example dinosaurs is the common ancestors of both birds
and reptiles. Thereby different paleontologists show different family trees for the same fossils.
Blast search engine
The above multicellular eukaryotic classification as per PSI-BLAST considerably along with
matrix -based alignments is used to reveal the amino acid substitution in every species for gene
expression similarity so that protein synthesis can be compared with every species in relation to
higher eukaryotes (chordates). PPSM (position specific scoring matrix) is widely used to get
either positive or negative results in relation to the substitution of the amino acids for protein
multiple sequences.
Delta Blast is more useful in detecting and is identifying “species proteins from lower
multicellular porifera species to annelids, arthropods, non-chordates & chordates” in which
amino acid or nucleotide sequences of the species, which are not closely related compared to the
PSI- BLAST. Some time PSI-Blast also enables to get possible information in identifying the
evolutionary nucleotide substituent’s in the species, which are not closely related.
Nervous system:
The three animal phyla that best represent stages in the evolution of the nervous system of
animals are animals belongs to primitive bilateria, Cnidaria and Ctenophora since these are often
referred as Epitheliozoa. These animals often diversified from primitive sponges where primitive
neuronal system has developed already. The nervous system present.
Exam 2 Study Guide. All questions will be over these concepts, voc.docxSANSKAR20
Exam 2 Study Guide. All questions will be over these concepts, vocabulary, and facts
Chp 10:
Cell Cycle
Genome
Mitosis
Chp11:
Meiosis
Gamete
Haploid & Diploid cell
Sexual reproduction
Chp12:
Gregor Mendel
Traits
Genotype & Phenotype
Allele
Dominant Trait & Recessive trait
Homozygous & Heterozygous
Punnet Square (concept. You will not do one on the exam)
Predictable Genetic frequencies (pedigree, farming genetic disorders)
Wild Type
Law of Segregation
Law of Independent assortment
Chp14:
DNA
Backbone
Nucleic Acid
Nucleotides
Base
Base Pair
Codon
Gene
Chromosome
DNA Polymerase (concept, vocab word)
Helicase (concept, vocab word)
Okazaki Fragment (concept, vocab word)
Proof Reading
Telomeres
DNA bases (4) and which bind
RNA: Uracil
Steps of DNA Replication (just listing the steps: min 5 max 10, depending on word choice)
Chp 15:
The Central Dogma of Biology
Transcription (steps, concepts)
Translation (steps, concepts)
tRNA
Mutation
Biotechnology
Chp 18:
Evolution
Natural Selection
Charles Darwin & Alfred R. Wallace
“Survival of the fittest” is incorrect.
Adaptation
Species
Hybrid (species): Postzygotic & Prezygotic
Speciation
Allopatric Speciation
Sympatric Speciation
Adaptive Radiation
Gradual Speciation & Punctuated Equilibrium
Chp 19:
Evolution
Evolution cumulative functions of: (know each)
Mutation, Genetic Drift, Migration, Natural Selection
Chance (involved with Evolution): Fixation, Founder Effect, Population Bottleneck
Natural Selection: 3 conditions for occurrence; what it looks like; what it does/does not do
Convergent Evolution
Evolution’s influence over, but not its “purpose”
Species are the basic unit of Biodiversity
Chp 20:
Phylogeny
Phylogenetic Trees/models
Concept of “shared ancestry”
Taxonomy: concept, define, & list 8 hierarchical categories
Convergent Evolution
Molecular Systematics & DNA Homology
Compare Phylogeny verse the “species concept”
Chp 21-29:
Biodiversity
Flora, Fauna, Biota
Virus (concept, importance to Evolution by Natural Selection)
Importance of “Domain”
Prokaryotes: Define, importance/role in Nature
Stromatolites as evidence
Biofilms
Protists: define, importance/role in Nature
Fungi: Define, importance/role in Nature
3 descriptors of Fungi
Fungal DNA
Hyphae & Mycelium
Decomposer
Mycorrhizae
Plants:
Ancestry (phylogeny)
Plants: Define, importance/role in nature
3 defining descriptors of Plants
Specific adaptations for evolution to land
3 problems all plants (as a phylogenetic group) face
Non-vascular Plant
Vascular Plant
Vascular Seed Plant
Vascular Tissue: Xylem & Phloem
Roots, True leaves
Waxy Cuticle
Important role of Ecological Succession of Plants to Life
Seed Plants:
Seed: define, role/importance of to a plant, water & reproduction
Spermatophytes
Gymnosperm
Angiosperm,
Flower & Fruit
Flower: Stamen, Carpel, Petal, Ovary)
Herbivory
Pollination & Pollinators: Trickery, Bribery, coevolution of
Importance of Plants to Humans
Humans and Plants coevolution
The life of a bee is very different f ...
Species delimitation - species limits and character evolutionRutger Vos
Lecture slides for the program orientation Evolutionary Biology at the Institute of Biology Leiden, the Netherlands. Thursday, September 7th, 2017.
Lecture notes are here: https://docs.google.com/document/d/e/2PACX-1vRIv5mKK1fjBby--u97emC7hrqXUbxFQZe63P1FpguuhHLG6xykbwXKeKXCUE5W-LSpakXYCI621xCK/pub
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Budding or Anagenesis? Paraphylyand Ancestor-Descendant Relationships from Tip-Dating Phylogenies of Fossil Lineages
1. Budding or Anagenesis?
Paraphyly and
Ancestor-Descendant Relationships
from Tip-Dating Phylogenies of
Fossil Lineages
David Bapst & Sandra Carlson
University of California Davis
Evolution 2017 Portland
Sunday, June 25th Feel free to
tweet this talk!
@dwbapst
2. The Question of Ancestors
in the Fossil Record
Fortey and Cooper 1986
3. Morphotaxa in
the Fossil Record
• Often, we find specimens
of varying age with similar
morphology
• We use those features to
define morphotaxa
spanning geologic time
Dicellograptus
4. • Interpret occurrences as a
chain of direct ancestor-
descendant relationships
• Central assumption since the
dawn of paleontology, critical
to biostratigraphy
… and rarely tested
Dicellograptus
The Most Fundamental
Assumption in Paleontology?
5. Maletz & Mitchell (1996)
Qualitative Interpretations of
Ancestor-Descendant Relationships
Among Morphotaxa
Kennett and Srinivasan (1983)
from Pearson (1998)
May Read the Fossil Record Too Literally
6. The problem is, very rarely
can we read the fossil
record as literally as this
7. How do we infer the
relationships among
ancestors & their descendants,
given the incompleteness
of the fossil record?
8. Stratocladistic Methods
Attempted To Make This More Rigorous
Bloch et al., 2001
• Treated implied gaps in
the fossil record as
interchangeable with
character changes under
maximum parsimony
(Fisher, 1991; 1994)
9. Bayesian sampled-ancestor tip-dating
• Infer dated phylogenies under a model of morph
character change, and under a formal model of
diversification and incompleteness of rock record:
the Fossilized Birth-Death Model (Heath et al., 2014)
• Taxa, as point occurrences in time, potentially placed
as sampled-ancestors (Gavryushkina et al., 2014)
Gavryushkinaetal.,2014
10. In The Age Of Ancestor Inference…
Beast2
(PP)
MrBayes
(PP)
cal3
(prop)
Bapst&Hopkins,2017,Paleobio.
(cal3 is an off-brand
tip-dating lite)
• Different methods agree on
placing ancestors [dinosaurs]
• Quantitative inferences agree with
previous putative pairs of
ancestor-descendants [trilobites]
Bapst,Wright,Matzke&Lloyd,2016.Biol.Lett.
11. Static Morphotaxa vs. Points in Time
• Morphotaxa in most fossil-rich groups are not
point occurrences in time (even many dinosaurs have
stratigraphic durations)
• Most studies have treated taxa with durations as a single
occurrence in time, usually earliest (first) occurrence
• Despite FBD assuming every sampled occurrence counted
• What happens with datasets where individual
occurrences are the operational taxon units?
• What happens if we treat individual morphotaxa as
multiple operational taxon units?
Allow us to test for a range of ancestral relationships
16. Time (Mya)
Tip-Dating Ostracod Occurrences
3 previously defined
morphospecies are
paraphyletic
(budding!)
12 sampled ancestors
Bapst, in prep.
17. Tip-Dating with
First and Last Occurrences
• A kludge: Duplicate character data for each taxon, put
separate uniform age priors for first and last occurrences
• thus doubling the number of tips
• Genus-level analyses for three groups of mid-Paleozoic
brachiopods: Terebratulides, Pentamerides, and
Stenoscismatoids (Carlson & Fitzgerald, 2008; Carlson, unpub.)
• Wrote R functions for automating and streamlining
creating NEXUS files with MrBayes blocks for tip-dating,
including analyses with empty matrices and topological
constraints
• https://github.com/dwbapst/paleotree
19. 10-50% of OTUs as Sampled Ancestors
Values Across the Post-Burnin Posteriors
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.
20. About 25% of SA are Last Occurrences:
10-22% Upper Limit on Anagenesis
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.
21. Majority of SA are First Occ. As Ancestors
to Last Occ. (Especially in Pentamerides)
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.
22. Budding (Paraphyletic Taxa) 2-4x More Common
Among Terebratulides and Stenoscismatoids
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.
23. A New Era of Ancestors on Trees
• Treating fossil morphotaxa as more than single OTUs sheds
light on patterns of ancestor-descendant relationships
• Earliest occurrences are frequently sampled ancestors to
their last occurrence, reaffirming that morphotaxa are often
ancestor-descendant sequences (but maybe not always)
• Budding likely more common than anagenesis:
10-22% of last occ. as SA (= maximum anagenesis), but
paraphyletic taxa mostly as common (= minimum budding)
• Ancestor-descendant relationships varied in pattern
(esp. Pentam. vs other groups)
This research was funded by
NSF grant EAR-1147537.
Thanks for listening! Questions?
24.
25.
26. Gaps in Densely-Sampled
Fossil Records
Maletz and Zhang, 2003; Vandenberg, 2003; C.E. Mitchell
• Closest relatives separated by a 15 to 20 million year gap in
this lineage:
• Were the intermediates living somewhere else? Open ocean?
Bergstromgraptus
Middle Darrwillian
Sinoretiograptus
Latest Katian
28. Tip-Dating with Mesozoic Theropods
• We used a somewhat infamous dataset to compare
tip-dating methods with cal3, for ancestor-
descendant relationships, divergence dating,
estimating evolutionary rates, etc...
• Do the methods agree?
• The support for particular taxa to be probable
ancestors were fairly correlated across methods
• So… Is Archaeopteryx really the ancestral bird?
Bapst, Wright, Matzke
& Lloyd, 2016; Biol. Lett.2. Ancestor-Descendants in the Fossil Record
with
April Wright Graeme LloydNick Matzke
29. • Significant rank-order pair-
wise correlations of
ancestral placement
between methods
• Strongest between MrBayes
and BEAST2
• Considerable differences
despite similar model
• Median # of ancestors per
tree for tip-dating = 1-2
• With cal3 (using entire
taxon durations) = 17
• Always buddingBeast2
(PP)
MrBayes
(PP)
cal3
(prop)
Bapst, Wright, Matzke & Lloyd, 2016
30. Whither the Ancestral Bird?
• Archaeopteryx rarely placed as a sampled ancestor
• Never placed as ancestor on lineage leading to
extant birds, but rather as a sampled ancestor to its
sister taxon / possible synonym Wellnhoferia
Bapst, Wright, Matzke & Lloyd, 2016
31. Case 1:
Cambrian pterocephaliid trilobites
• Hopkins (2011) did a cladistic analysis and reviewed
a number of (qualitative) ancestor-descendant
pairs previously suggested for this group
• Does cal3 find support for those pairs, and does it
match the mode inferred by previous authors?
• Apply cal3 to the single maximum-parsimony topology &
100 CONOP solutions from Hopkins (2011)
• Obtained 100 dated phylogenies, quantified support for
a given AD pair as the proportion of trees
Bapst & Hopkins, now in press at Paleobiology!
32. Each pair is a
stacked barplot
Dots indicate
putative pairs
Evidence for all
a priori AD pairs,
& a few extra
cal3 finds very
little support for
anagenesis
Given biases,
perhaps entirely
budding?
33. • Each pair is a
stacked barplot
• Dots indicate
putative pairs
• Support for all
a priori AD pairs,
& a few extra
• cal3 finds very
little support for
anagenesis
• Support for budding
suggests globally
instantaneous origins
of new morphotaxa
2. Ancestor-Descendants in the Fossil Record