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HaplowebMaker & CoMa: delimiting species using
haplowebs and conspecificity matrices
28.07.2020
−2 0 2 4 6 8 10 12
Bono
Catherine
Joey
Kombate
Sandy
Ulindi
Yasa
Kosana
Zorba
Clara
Louise
Marco
Akila
Alley
Amizero
Annie
Eva
Judy
Mary
Mimi
Mzee
Sultana
Chiquita
Dodo
Henri
Ivindo
Makata
Masuku
Moanda
Noemie
Ntoum
Frits
Hilko
Oscar
Socrates
Sonja
Yoran
Regina
Yvonne
Yvonne
Regina
Yoran
Sonja
Socrates
Oscar
Hilko
Frits
Ntoum
Noemie
Moanda
Masuku
Makata
Ivindo
Henri
Dodo
Chiquita
Sultana
Mzee
Mimi
Mary
Judy
Eva
Annie
Amizero
Alley
Akila
Marco
Louise
Clara
Zorba
Kosana
Yasa
Ulindi
Sandy
Kombate
Joey
Catherine
Bono
−2 0 2 4 6 8 10 12
Yann Spöri & Jean-François Flot (ULB, Belgium)
Spöri & Flot (2020) Methods in Ecology and Evolution
https://eeg-ebe.github.io/HaplowebMaker/
https://eeg-ebe.github.io/CoMa/
Petzold &Hassanin (2020) PLoS ONE
S
Species delimitation’s pitfalls
Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be)
Allelic monophyly (the alleles of
each species form a clade).!
!
!
!
Allelic exclusivity (the species do
not share any identical allele)
12 22 32 42 52 62
T2: two species
11 21 31 41
51 61
T1: two species
speciation
10 20 30 40
50 60
: mutation
: extinction
T0: one species
n
Species are frequently expected to be monophyletic in gene trees, and to display intraspecific
distances smaller than interspecific distances. Both assumptions, however, do not hold when
species are recently diverged and/or when effective population sizes are large.
Among single-locus species
delimitation approaches, tree-
based methods (GMYC, PTP, K/
θ,...) assume species to be
m o n o p h y l e t i c , w h e r e a s
distance-based methods (DNA
barcoding, ABGD,..) assume that
interspecific distances are
separated from intraspecific
ones by a barcoding gap. By
contrast, allele sharing-based
approaches (such as haplowebs)
do no rely on such assumptions.
MEIOSCOOL
Guidelines for DNA taxonomy, with a focus on the meiofauna
Diego Fontaneto & Jean-François Flot & Cuong Q. Tang
Mar Biodiv (2015) 45:433–451
DOI 10.1007/s12526-015-0319-7
HaplowebMaker: a web tool to generate haplowebs
https://eeg-ebe.github.io/HaplowebMaker/
Haplotype webs (in short, haplowebs) are
used to display at the same time the
evolutionary relationships between nuclear
haplotypes and their co-occurrence in
heterozygous individuals. Using haplowebs,
putative species are immediately apparent as
connected groups of haplotypes.!
HaplowebMaker is the first tool available that
can generate haplowebs automatically.!
A median-joining network is first calculated then
visualized using a force-directed graph-drawing
algorithm. In a later step, Bezier curves are added in
order to represent haplotypes co-occurring in
heterozygous individuals.!
The resulting haploweb can be edited using a dedicated
module before being exported as SVG or printed as PDF.
If several markers were inputted, a partition matrix is
also produced recapitulating all results.
PCR
products
homozygotes (trivial cases)
heterozygotes with one SNP
(trivial cases)
numerous double peaks
heterozygotes with two haplotypes of
different lengths (use Champuru)
pairs of forward and
reverse chromatograms
a few double peaks
heterozygotes with several SNPs but
no indels (use SeqPHASE)
DNA
extracts
one double peak
no double peaks
Ind1a
Ind3a
Ind2
Ind1b
Ind3b
Ind4a
Ind6
Ind5
Ind4b
Ind7a
Ind7b
Ind9
Ind8b
Ind8a
result: a phased dataset
of allelic sequences
next-generation
sequencing
(e.g. RADseq,
capture,...)
Individual1_a!
Individual1_b!
Individual2!
Individual3_a!
Individual3_b!
Individual4_a!
Individual4_b!
Individual5!
Individual6!
Individual7_a!
Individual7_b!
Individual8_a!
Individual8_b!
Individual9!
Champuru: available at http://jfflot.mnhn.fr/champuru/!
SeqPHASE: available at https://eeg-ebe.github.io/SeqPHASE/ e.github.io/HaplowebMaker/
Examples of outputs
Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be)
Individual2
dual2
Individual1
dual1
Individual3
dual3
Individual4
dual4
Individual5
dual5
Individual9
dual9
Individual8
dual8
Individual7
dual7
Individual6
dual6
CoMa: a web tool to generate conspecificity matrices
A conspecificity matrix is a square matrix
displaying the conspecificity scores of
every pair of invididual in a dataset.
Conspecificity scores can be calculated as
the number of lines of evidence (e.g.,
markers) supporting the conspecificity of a
pair of individuals minus the number of lines
of evidence indicated they belong to
different species (i.e., are heterospecific).
CoMa takes as input a partition matrix (in which
each column represents a partition of the dataset
according to one source of information or
delimitation method) and outputs a conspecificity
matrix (with individuals reordered to reveal species
as squares of high conspecificity scores along the
diagonal). In additional to the numerical matrix (as
a tab-delimited text file), it also output a graphical
SVG version for immediate visualization.!
https://eeg-ebe.github.io/HaplowebMaker/
Examples of outputs
Petzold &Hassanin (2020) PLoS ONE
A
D
B
F
E
C
Debortoli et al. (2016) Current Biology
Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be)
Partition matrix obtained from HaplowebMaker
https://eeg-ebe.github.io/CoMa/marker A
marker B
marker C
A B C
Individual 1 1 1 1
Individual 2 1 1 1
Individual 3 1 1 2
Individual 4 1 1 3
Individual 5 2 2 4
Individual 6 2 3 5
Individual 7 2 3 5
Individual 8 2 3 5
Individual 9 2 4 6
weights 1 1 1
Haplowebs for three diploid DNA
markers sequenced for nine individuals
Real-life example: delineating bonobos from chimps using HaplowebMaker and CoMa
https://commons.wikimedia.org/wiki/File:Schimpanse,_Pan_troglodytes_3.JPG
https://commons.wikimedia.org/wiki/File:Apeldoorn_Apenheul_zoo_Bonobo.jpg)
−2 0 2 4 6 8 10 12
Bono
Catherine
Joey
Kombate
Sandy
Ulindi
Yasa
Kosana
Zorba
Clara
Louise
Marco
Akila
Alley
Amizero
Annie
Eva
Judy
Mary
Mimi
Mzee
Sultana
Chiquita
Dodo
Henri
Ivindo
Makata
Masuku
Moanda
Noemie
Ntoum
Frits
Hilko
Oscar
Socrates
Sonja
Yoran
Regina
Yvonne
Yvonne
Regina
Yoran
Sonja
Socrates
Oscar
Hilko
Frits
Ntoum
Noemie
Moanda
Masuku
Makata
Ivindo
Henri
Dodo
Chiquita
Sultana
Mzee
Mimi
Mary
Judy
Eva
Annie
Amizero
Alley
Akila
Marco
Louise
Clara
Zorba
Kosana
Yasa
Ulindi
Sandy
Kombate
Joey
Catherine
Bono
−2 0 2 4 6 8 10 12
https://commons.wikimedia.org/wiki/File:Schimpanse,_Pan_troglodytes_3.JPG https://commons.wikimedia.org/wiki/File:Apeldoorn_Apenheul_zoo_Bonobo.jpg)
Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be)
Resulting conspecificity matrix (clustered using heatmap3)
Dataset from Fischer et al. (2006) Current Biology re-analyzed in Dellicour & Flot (2015) Systematic Biology and in Spöri & Flot (2020) Methods in Ecology and Evolution
12 nuclear loci sequenced for 30 chimpanzees (10 from each of three subspecies) and nine bonobos

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HaplowebMaker & CoMa: delimiting species using haplowebs and conspecificity matrices

  • 1. HaplowebMaker & CoMa: delimiting species using haplowebs and conspecificity matrices 28.07.2020 −2 0 2 4 6 8 10 12 Bono Catherine Joey Kombate Sandy Ulindi Yasa Kosana Zorba Clara Louise Marco Akila Alley Amizero Annie Eva Judy Mary Mimi Mzee Sultana Chiquita Dodo Henri Ivindo Makata Masuku Moanda Noemie Ntoum Frits Hilko Oscar Socrates Sonja Yoran Regina Yvonne Yvonne Regina Yoran Sonja Socrates Oscar Hilko Frits Ntoum Noemie Moanda Masuku Makata Ivindo Henri Dodo Chiquita Sultana Mzee Mimi Mary Judy Eva Annie Amizero Alley Akila Marco Louise Clara Zorba Kosana Yasa Ulindi Sandy Kombate Joey Catherine Bono −2 0 2 4 6 8 10 12 Yann Spöri & Jean-François Flot (ULB, Belgium) Spöri & Flot (2020) Methods in Ecology and Evolution https://eeg-ebe.github.io/HaplowebMaker/ https://eeg-ebe.github.io/CoMa/ Petzold &Hassanin (2020) PLoS ONE S
  • 2. Species delimitation’s pitfalls Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be) Allelic monophyly (the alleles of each species form a clade).! ! ! ! Allelic exclusivity (the species do not share any identical allele) 12 22 32 42 52 62 T2: two species 11 21 31 41 51 61 T1: two species speciation 10 20 30 40 50 60 : mutation : extinction T0: one species n Species are frequently expected to be monophyletic in gene trees, and to display intraspecific distances smaller than interspecific distances. Both assumptions, however, do not hold when species are recently diverged and/or when effective population sizes are large. Among single-locus species delimitation approaches, tree- based methods (GMYC, PTP, K/ θ,...) assume species to be m o n o p h y l e t i c , w h e r e a s distance-based methods (DNA barcoding, ABGD,..) assume that interspecific distances are separated from intraspecific ones by a barcoding gap. By contrast, allele sharing-based approaches (such as haplowebs) do no rely on such assumptions. MEIOSCOOL Guidelines for DNA taxonomy, with a focus on the meiofauna Diego Fontaneto & Jean-François Flot & Cuong Q. Tang Mar Biodiv (2015) 45:433–451 DOI 10.1007/s12526-015-0319-7
  • 3. HaplowebMaker: a web tool to generate haplowebs https://eeg-ebe.github.io/HaplowebMaker/ Haplotype webs (in short, haplowebs) are used to display at the same time the evolutionary relationships between nuclear haplotypes and their co-occurrence in heterozygous individuals. Using haplowebs, putative species are immediately apparent as connected groups of haplotypes.! HaplowebMaker is the first tool available that can generate haplowebs automatically.! A median-joining network is first calculated then visualized using a force-directed graph-drawing algorithm. In a later step, Bezier curves are added in order to represent haplotypes co-occurring in heterozygous individuals.! The resulting haploweb can be edited using a dedicated module before being exported as SVG or printed as PDF. If several markers were inputted, a partition matrix is also produced recapitulating all results. PCR products homozygotes (trivial cases) heterozygotes with one SNP (trivial cases) numerous double peaks heterozygotes with two haplotypes of different lengths (use Champuru) pairs of forward and reverse chromatograms a few double peaks heterozygotes with several SNPs but no indels (use SeqPHASE) DNA extracts one double peak no double peaks Ind1a Ind3a Ind2 Ind1b Ind3b Ind4a Ind6 Ind5 Ind4b Ind7a Ind7b Ind9 Ind8b Ind8a result: a phased dataset of allelic sequences next-generation sequencing (e.g. RADseq, capture,...) Individual1_a! Individual1_b! Individual2! Individual3_a! Individual3_b! Individual4_a! Individual4_b! Individual5! Individual6! Individual7_a! Individual7_b! Individual8_a! Individual8_b! Individual9! Champuru: available at http://jfflot.mnhn.fr/champuru/! SeqPHASE: available at https://eeg-ebe.github.io/SeqPHASE/ e.github.io/HaplowebMaker/ Examples of outputs Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be)
  • 4. Individual2 dual2 Individual1 dual1 Individual3 dual3 Individual4 dual4 Individual5 dual5 Individual9 dual9 Individual8 dual8 Individual7 dual7 Individual6 dual6 CoMa: a web tool to generate conspecificity matrices A conspecificity matrix is a square matrix displaying the conspecificity scores of every pair of invididual in a dataset. Conspecificity scores can be calculated as the number of lines of evidence (e.g., markers) supporting the conspecificity of a pair of individuals minus the number of lines of evidence indicated they belong to different species (i.e., are heterospecific). CoMa takes as input a partition matrix (in which each column represents a partition of the dataset according to one source of information or delimitation method) and outputs a conspecificity matrix (with individuals reordered to reveal species as squares of high conspecificity scores along the diagonal). In additional to the numerical matrix (as a tab-delimited text file), it also output a graphical SVG version for immediate visualization.! https://eeg-ebe.github.io/HaplowebMaker/ Examples of outputs Petzold &Hassanin (2020) PLoS ONE A D B F E C Debortoli et al. (2016) Current Biology Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be) Partition matrix obtained from HaplowebMaker https://eeg-ebe.github.io/CoMa/marker A marker B marker C A B C Individual 1 1 1 1 Individual 2 1 1 1 Individual 3 1 1 2 Individual 4 1 1 3 Individual 5 2 2 4 Individual 6 2 3 5 Individual 7 2 3 5 Individual 8 2 3 5 Individual 9 2 4 6 weights 1 1 1 Haplowebs for three diploid DNA markers sequenced for nine individuals
  • 5. Real-life example: delineating bonobos from chimps using HaplowebMaker and CoMa https://commons.wikimedia.org/wiki/File:Schimpanse,_Pan_troglodytes_3.JPG https://commons.wikimedia.org/wiki/File:Apeldoorn_Apenheul_zoo_Bonobo.jpg) −2 0 2 4 6 8 10 12 Bono Catherine Joey Kombate Sandy Ulindi Yasa Kosana Zorba Clara Louise Marco Akila Alley Amizero Annie Eva Judy Mary Mimi Mzee Sultana Chiquita Dodo Henri Ivindo Makata Masuku Moanda Noemie Ntoum Frits Hilko Oscar Socrates Sonja Yoran Regina Yvonne Yvonne Regina Yoran Sonja Socrates Oscar Hilko Frits Ntoum Noemie Moanda Masuku Makata Ivindo Henri Dodo Chiquita Sultana Mzee Mimi Mary Judy Eva Annie Amizero Alley Akila Marco Louise Clara Zorba Kosana Yasa Ulindi Sandy Kombate Joey Catherine Bono −2 0 2 4 6 8 10 12 https://commons.wikimedia.org/wiki/File:Schimpanse,_Pan_troglodytes_3.JPG https://commons.wikimedia.org/wiki/File:Apeldoorn_Apenheul_zoo_Bonobo.jpg) Yann Spöri (yspori@ulb.ac.be) & Jean-François Flot (jflot@ulb.ac.be) Resulting conspecificity matrix (clustered using heatmap3) Dataset from Fischer et al. (2006) Current Biology re-analyzed in Dellicour & Flot (2015) Systematic Biology and in Spöri & Flot (2020) Methods in Ecology and Evolution 12 nuclear loci sequenced for 30 chimpanzees (10 from each of three subspecies) and nine bonobos