Presentation of the models of gene duplication, transfer, loss, and incomplete lineage sorting developed by my colleagues and myself. Results on gene tree inference, species tree inference are presented. Groups of species studied include mammals, birds, fungi and cyanobacteria.
Presentation of PHYLDOG, a piece of software for reconstructing gene and species phylogenies, with a focus on the practical side of things and pointers to a tutorial.
Towards inferring the history of life in the presence of lateral gene transfe...boussau
Short presentation given at Evolution 2014 (similar to that given at SMBE 2014). Introduces a new method for estimating a species tree in the presence of gene duplication, loss, and lateral gene transfer, in a statistical framework, based on a large number of gene families. Results on simulations and real data are presented.
Overview of the approaches I co-developed to reconstruct species trees and gene trees, in the presence of gene duplications, losses and transfers, or incomplete lineage sorting. Includes Phyldog, ALE, MP-EST*, RevBayes.
The Role of Libraries in Data Management and CurationNicole Vasilevsky
The Role of Libraries in Data Management and Curation, presented at the American Library Association conference in Las Vegas, NV, 07/29/14.
Abstract:
As increasing amounts of data are being generated, applying best practices in handling data is important, and librarians are well poised to assist users. During this session, we will discuss the role of libraries in assisting with data management, application of metadata, ontologies, data standards, and the publication of data in repositories and on the Semantic Web. This talk will describe best data practices and engage the attendees in interactive activities to demonstrate these principles.
Keynote presentation from Plant and Pathogen Bioinformatics workshop at EMBL-EBI, 8-11 July 2014
Slides and teaching material are available at https://github.com/widdowquinn/Teaching-EMBL-Plant-Path-Genomics
Presentation of PHYLDOG, a piece of software for reconstructing gene and species phylogenies, with a focus on the practical side of things and pointers to a tutorial.
Towards inferring the history of life in the presence of lateral gene transfe...boussau
Short presentation given at Evolution 2014 (similar to that given at SMBE 2014). Introduces a new method for estimating a species tree in the presence of gene duplication, loss, and lateral gene transfer, in a statistical framework, based on a large number of gene families. Results on simulations and real data are presented.
Overview of the approaches I co-developed to reconstruct species trees and gene trees, in the presence of gene duplications, losses and transfers, or incomplete lineage sorting. Includes Phyldog, ALE, MP-EST*, RevBayes.
The Role of Libraries in Data Management and CurationNicole Vasilevsky
The Role of Libraries in Data Management and Curation, presented at the American Library Association conference in Las Vegas, NV, 07/29/14.
Abstract:
As increasing amounts of data are being generated, applying best practices in handling data is important, and librarians are well poised to assist users. During this session, we will discuss the role of libraries in assisting with data management, application of metadata, ontologies, data standards, and the publication of data in repositories and on the Semantic Web. This talk will describe best data practices and engage the attendees in interactive activities to demonstrate these principles.
Keynote presentation from Plant and Pathogen Bioinformatics workshop at EMBL-EBI, 8-11 July 2014
Slides and teaching material are available at https://github.com/widdowquinn/Teaching-EMBL-Plant-Path-Genomics
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor Michel
Global Digital Infrastructure for Biological Nomenclature and Taxonomy
Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, (e.michel@nhm.ac.uk)
Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA
Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA
Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK,
The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor Michel
Global Digital Infrastructure for Biological Nomenclature and Taxonomy
Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, (e.michel@nhm.ac.uk)
Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA
Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA
Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK,
The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
Cave animals at the dawn of speleogenomicsfriedrichwsu
Presentation on the application and impact of next generation sequencing in studies of cave animals and other subterranean species. Held at the 23rd International Conference on Subterranean Biology in the Department of Biology at the University of Arkansas, 13-17 June 2016, Fayetteville, Arkansas.
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 IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Models of gene duplication, transfer and loss to study genome evolution
1. Bastien Boussau
LBBE, CNRS, Université de Lyon
Models of gene
duplication, transfer and loss
to study genome evolution
2. Collaborators
Lyon collaborators:
• Adrián Arellano Davín
• Gergely Szöllősi (Budapest)
• Vincent Daubin
• Eric Tannier
• Thomas Bigot
• Magali Semeria
• Manolo Gouy
• Laurent Duret
• Nicolas Lartillot
Austin/Illinois collaborators:
• Siavash Mirarab
• Md. Shamsuzzoha Bayzid
• Tandy Warnow
RevBayes collaborators:
• Sebastian Hoehna
• Michael Landis
• Tracy Heath
• Fredrik Ronquist
• Brian Moore
• John Huelsenbeck
• …
3. Plan
1. Gene duplications and losses
• Mammalian genomes
2. Gene duplications, losses and transfers
• Fungi and Cyanobacteria
3. A fast approach to dealing with incomplete
lineage sorting
• Birds
4. 2 vignettes
4. To study genome evolution:
1. One species tree:
!
!
!
2. Thousands of gene trees:
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
5. To study genome evolution:
1. One species tree:
!
!
!
2. Thousands of gene trees:
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
7. Why
our
current
pipeline
can
be
improved
•Gene
alignments:
•Error
prone
(Genes
are
short)
•Point
es:mates
8. Why
our
current
pipeline
can
be
improved
•Gene
trees:
•based
on
alignments
•Point
es:mates
•Gene
alignments:
•Error
prone
(Genes
are
short)
•Point
es:mates
9. Why
our
current
pipeline
can
be
improved
•Gene
trees:
•based
on
alignments
•Point
es:mates
•Species
trees:
•based
on
gene
trees
•Gene
alignments:
•Error
prone
(Genes
are
short)
•Point
es:mates
10. Why
our
current
pipeline
can
be
improved
•Gene
trees:
•based
on
alignments
•Point
es:mates
•Species
trees:
•based
on
gene
trees
•Gene
alignments:
•Error
prone
(Genes
are
short)
•Point
es:mates
11. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
12. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
13. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
14. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D
15. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D DL
16. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGTD DL
17. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILSD DL
18. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL: Boussau et al., Genome Research 2013
D DL
19. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013
20. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013
21. (thousands
of
alignments)
PHYLDOG
All gene families
Rooted species tree,
numbers of duplications
and losses,
rooted gene trees D1
D2
D3
D4
D5
D6
L2
L1
L4
L3
L5
L6
Joint reconstruction of
the species tree,
gene trees, and
numbers of duplications and losses
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D1
D3
D2 D4
D5 D6
L1
L3
L2 L4
L5 L6
Boussau et al., Genome Research 2013
22. (thousands
of
alignments)
PHYLDOG
All gene families
Rooted species tree,
numbers of duplications
and losses,
rooted gene trees D1
D2
D3
D4
D5
D6
L2
L1
L4
L3
L5
L6
Joint reconstruction of
the species tree,
gene trees, and
numbers of duplications and losses
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D1
D3
D2 D4
D5 D6
L1
L3
L2 L4
L5 L6
Probabilis5c
models:
• sequence
evolu1on
• gene
family
evolu1on
Boussau et al., Genome Research 2013
23. PHYLDOG: a model of
gene duplication and loss
Assumptions!
•Genes evolve along the species tree:!
•birth events:!
•duplications (rate of duplication)!
•death events:!
•losses (rate of loss)!
•Each gene family is independent of other genes!
•Each gene copy is independent of other copies!
!
!
24. Study
of
mammalian
genome
evolu:on
10
• Challenging
but
well-‐studied
phylogeny
• 36
mammalian
genomes
available
in
Ensembl
v.
57
• About
7000
gene
families
• Correc:on
for
poorly
sequenced
genomes
26. Quality
of
the
gene
trees
12
Comparison
between:
PhyML
(used
for
the
PhylomeDB
and
Homolens
databases
)
TreeBeST
(used
for
the
Ensembl-‐Compara
database)
PHYLDOG
Two
approaches:
• Looking
at
ancestral
genome
sizes
• Assessing
how
well
one
can
recover
ancestral
syntenies
using
reconstructed
gene
trees
(Bérard
et
al.,
Bioinforma:cs
2012)
29. Recent improvements to PHYLDOG
• Easier installation using Cmake or a virtual machine!
• Better algorithms for gene tree inference!
• Better algorithm for starting species tree!
• Faster computations using the Phylogenetic Likelihood Library
(PLL, A. Stamatakis group)!
• Python scripts to help run the program
30. Plan
1. Gene duplications and losses
• Mammalian genomes
2. Gene duplications, losses and transfers
• Fungi and Cyanobacteria
3. A fast approach to dealing with incomplete
lineage sorting
• Birds
4. 2 vignettes
31. Species: A B C D
T
I
M
E
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
DL+T:!
Szöllősi et al. "
PNAS 2013
32. Species: A B C D
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013
33. Gene
transfers
and
the
quixo:c
pursuit
of
the
TOL
DooliYle
WF,
Science
1999
34. Gene
transfers
and
the
quixo:c
pursuit
of
the
TOL
DooliYle
WF,
Science
1999
35. Gene
transfers
and
the
quixo:c
pursuit
of
the
TOL
DooliYle
WF,
Science
1999
“The monistic concept of a single universal tree appears […]
increasingly obsolete. […][It is] no longer the most
scientifically productive position to hold[…][It] accounts for
only a minority of observations from genomes.”!
Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall,
Lapointe, Dupré, Dagan, Boucher, Martin, !
Biology Direct 2009.
36. exODT: a model of
gene duplication, transfer, and loss
Assumptions!
•Genes evolve along the species tree:!
•birth events:!
•duplications (rate of duplication)!
•transfers (rate of receiving a gene)!
•death events:!
•losses (rate of loss)!
•Each gene family is independent of other genes!
•Each gene copy is independent of other copies!
•Transfers can go through unsampled/extinct species!
!
!
37. exODT: a model of
gene duplication, transfer, and loss
Szöllősi et al., Syst. Biol. a 2013
38. exODT: a model of
gene duplication, transfer, and loss
Szöllősi et al., Syst. Biol. a 2013
39. Better gene trees, fewer transfers
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. b 2013
40. Better gene trees, fewer transfers
Usual
approach
ALE
+DTL
Transfereventsperfamily
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. b 2013
41. Application to real data:
Cyanobacteria and Fungi
Cyanobacteria!
• > 2.4 billion years old! !
• 40 species!
• 1,200 to 4,500 protein coding genes!
• 7,410 gene families!
!
Fungi (Dikarya)!
• ~ 1 billion years old!
• 28 species!
• 5,200 to 10,000 protein coding genes!
• 11,387 gene families!
!!
Both cases: !
• fixed species tree, gene trees inferred using the
Duplication, Transfer and Loss model! Szöllősi et al., under review
42. Application to real data:
Cyanobacteria and Fungi
Cyanobacteria!
• > 2.4 billion years old! !
• 40 species!
• 1,200 to 4,500 protein coding genes!
• 7,410 gene families!
!
Fungi (Dikarya)!
• ~ 1 billion years old!
• 28 species!
• 5,200 to 10,000 protein coding genes!
• 11,387 gene families!
!!
Both cases: !
• fixed species tree, gene trees inferred using the
Duplication, Transfer and Loss model!
Transfers are expected
Transfers should be less frequent
Szöllősi et al., under review
49. Comparing transfer rates
• Cyanobacteria and Fungi differ in their age:!
!
We can compare normalized numbers of events:!
T/(T+D)!
!
• The Cyanobacteria and Fungi data sets differ in their
number of species:!
!
We can perform rarefaction studies
Szöllősi et al., under review
58. Using transfers to date clades
?
T
I
M
E
Because we can identify gene transfers, we have information for
ordering the nodes of a species tree
59. Bayesian species tree inference
accounting for DTL events
• STRALE:
• A Bayesian probabilistic method that can interpret thousands of
gene trees in terms of:
• speciation events
• duplication events (D)
• transfer events (T)
• loss events (L)
• A method able to estimate the DTL rates
• A method able to reconstruct the species tree
• A method able to order the nodes of the species tree
61. Conclusion on DTL models
• The use of DTL models shows that the number of gene
transfers has so far been overestimated
• DTL models can be used to study genome evolution
and in particular rates of gene transfer
• DTL models can be used to date the nodes of a species
phylogeny
• DTL models should provide a powerful tool to infer an
accurate account of the history of life
62. Plan
1. Gene duplications and losses
• Mammalian genomes
2. Gene duplications, losses and transfers
• Fungi and Cyanobacteria
3. A fast approach to dealing with incomplete
lineage sorting
• Birds
4. 2 vignettes
63. Species: A B C D
T
I
M
E
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
DL+T:!
Szöllősi et al. "
PNAS 2013
64. Species: A B C D
T
I
M
E
LGT ILS
ILS: !
Mirarab et al.
Science 2014
DL: Boussau et al., Genome Research 2013
D DL
DL+T:!
Szöllősi et al. "
PNAS 2013
65. 35
The multispecies coalescent
Rannala and Yang, Genetics 2003
• Divergence times in the species tree!
• Divergence times in the gene trees!
• Effective population sizes in the species tree
66. Faster alternatives to the multispecies coalescent
use fixed gene trees
E.g.: MP-EST (Liu, Yu and Edwards, 2010)!
Input: fixed gene trees!
Output: species tree with branch lengths in coalescent units!
!
Has been shown to be consistent, under one notable assumption: !
gene trees are correct.
67. Errors in gene trees decrease the accuracy of
estimated species trees
Mirarab, Bayzid and Warnow, Syst. Biol 2014
76. 44Mirarab et al., PLoS One, accepted
Improving statistical binning: weighted statistical binning
Practice: weighted binning and unweighted binning have about the same
accuracy !
Theory: weighted statistical binning can be shown to be consistent,
unweighted statistical binning is not.
77. Plan
1. Gene duplications and losses
• Mammalian genomes
2. Gene duplications, losses and transfers
• Fungi and Cyanobacteria
3. A fast approach to dealing with incomplete
lineage sorting
• Birds
4. 2 vignettes
78. RevBayes
• R-like language
• Model-based phylogenetics
• Many models of sequence evolution
• Models for dating
• Models for phylogeography
• Models for continuous traits
• Models for gene tree/species tree inference
• http://revbayes.net
• Sebastian Hoehna
• Michael Landis
• Tracy Heath
• Fredrik Ronquist
• Nicolas Lartillot
• Brian Moore
• John Huelsenbeck
• …
82. Conclusions
• We develop methods for gene tree and species
tree inference
• Improvement of gene trees and species trees in the
presence of:
• duplications and losses,
• transfers,
• incomplete lineage sorting
• Parallel algorithms applicable to genome-scale data
• We study the evolution of life, ancient and recent
83. RevBayes collaborators:
• Sebastian Hoehna
• Michael Landis
• Tracy Heath
• Fredrik Ronquist
• Brian Moore
• John Huelsenbeck
• …
Lyon collaborators:
• Adrián Arellano Davín
• Gergely Szöllősi (Budapest)
• Vincent Daubin
• Eric Tannier
• Thomas Bigot
• Magali Semeria
• Manolo Gouy
• Laurent Duret
• Nicolas Lartillot
Austin/Illinois collaborators:
• Siavash Mirarab
• Md. Shamsuzzoha Bayzid
• Tandy Warnow
Thanks!
