renesance druhové delimitace: změna druhového konceptu u ... · konceptu u rodu aspergillus ......
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Renesance druhovédelimitace:
změna druhového
konceptu
u rodu Aspergillus
František Sklenář[email protected]
Proč renesance?
Renesance
Renesance
„a new growth of activity or interest insomething, especially art, literature, or music“
Články o renesanci delimitace druhů
Sites et Marshall (2003)634
Články o renesanci delimitace druhů
Camargo et Sites (2013)
Články o renesanci delimitace druhů
Flot (2015)
Renesance druhové delimitace
Flot (2015)
Po
če
t člá
nků
s k
líčo
vým
slo
ve
m v
ná
zvu
Rok
Renesance druhové delimitace
Po
če
t člá
nků
s k
líčo
vým
slo
ve
m v
ná
zvu
Rok
Speciace, druhové
koncepty a delimitace
druhů
Druhové koncepty podle Zachos (2016)
Agamospeices C
Biological SC
Biosimilarity SC
Cladistic SC
Cohesion SC
Compilospecies C
Differential Fitness SC
Ecological SC
Evolutionary Significant Unit
Evolutionary SC
Genealogical SC
Genealogical Concordance SC
General Lineage SC
Genetic SC
Genic SC
Genotypic Cluster SC
Hennigian SC
Internodal SC
Least Inclusive Taxonomic Unit
Morphological SC
Non-dimensional SC
Nothospecies C
Phenetic SC
Phylogenetic SC (diagnosibility version)
Phylo-Phenetic SC
Pragmatic SC
Recognition SC
Reproductive competition SC
Successional SC
Taxonomic SC
Unified SC
Phylogenetic SC (monophyly version)
Druhové koncepty podle Zachos (2016)
Agamospeices C
Biological SC
Biosimilarity SC
Cladistic SC
Cohesion SC
Compilospecies C
Differential Fitness SC
Ecological SC
Evolutionary Significant Unit
Evolutionary SC
Genealogical SC
Genealogical Concordance SC
General Lineage SC
Genetic SC
Genic SC
Genotypic Cluster SC
Hennigian SC
Internodal SC
Least Inclusive Taxonomic Unit
Morphological SC
Non-dimensional SC
Nothospecies C
Phenetic SC
Phylogenetic SC (diagnosibility version)
Phylo-Phenetic SC
Pragmatic SC
Recognition SC
Reproductive competition SC
Successional SC
Taxonomic SC
Unified SC
Phylogenetic SC (monophyly version)
32
Druhové koncepty podle Zachos (2016)
Agamospeices C
Biological SC
Biosimilarity SC
Cladistic SC
Cohesion SC
Compilospecies C
Differential Fitness SC
Ecological SC
Evolutionary Significant Unit
Evolutionary SC
Genealogical SC
Genealogical Concordance SC
General Lineage SC
Genetic SC
Genic SC
Genotypic Cluster SC
Hennigian SC
Internodal SC
Least Inclusive Taxonomic Unit
Morphological SC
Non-dimensional SC
Nothospecies C
Phenetic SC
Phylogenetic SC (diagnosibility version)
Phylo-Phenetic SC
Pragmatic SC
Recognition SC
Reproductive competition SC
Successional SC
Taxonomic SC
Unified SC
Phylogenetic SC (monophyly version)
32
Druhové koncepty - terminologie
species concept
species criterion
species recognition
Unified Species ConceptDe Queiroz (2007)
2 linie, které se vyvíjejí
odděleně
Species delimitation – třídění
metod podle Sites et Marshall (2003)
Tree-based
Non-tree based
Species delimitation – třídění
metod podle Carstens et al (2013)
Species delimitation (species hypothesis)
Species tree
Species validation546
Renesance druhové delimitace
Po
če
t člá
nků
s k
líčo
vým
slo
ve
m v
ná
zvu
Rok
546
Wright-Fisher model
čas
Wright-Fisher model
čas
Wright-Fisher model
čas
Wright-Fisher model
čas
Wright-Fisher model
čas
Wright-Fisher model
čas
Wright-Fisher model
čas
Multicpecies coalescent model
(MSC)
čas
Multicpecies coalescent model
(MSC)
τ0 - čas od oddělení linií
θ - velikost populací
Species delimitation – třídění
metod podle Carstens et al (2013)
Species delimitation (species hypothesis)
Species tree
Species validation
GMYC, PTP, STACEY, CLADES, ABGD, Brownie, STRUCTURE, GENELAND
*BEAST, BEST, BUCKy, ASTRAL, GLASS, SNAPP
BP&P, PHRAPL, GSI, spedeSTEM
Species delimitation
vnitrodruhová variabilitaLim et al.(2012)
Ahrens et al.(2016)
Species delimitation
(species hypothesis)
GMYC (Fujisawa et Barraclough 2013)
bGMYC (Reid et Carstens 2012)
PTP, bPTP (Zhang et al. 2013)
STACEY (Jones 2016)
ABGD (Puillandre et al. 2012)
Geneland
Brownie
CLADES (Pei et al. 2018)
Ultrametrický strom
GMYC
Ultrametrický strom
bGMYC
Species delimitation
(species hypothesis)
GMYC (Fujisawa et Barraclough 2013)
bGMYC (Reid et Carstens 2012)
PTP, bPTP (Zhang et al. 2013)
STACEY (Jones 2016)
ABGD (Puillandre et al. 2012)
Geneland
Brownie
ABGD
Puillandre et al. (2012)
Species delimitation
(species hypothesis)
GMYC (Fujisawa et Barraclough 2013)
bGMYC (Reid et Carstens 2012)
PTP, bPTP (Zhang et al. 2013)
STACEY (Jones 2016)
ABGD (Puillandre et al. 2012)
Geneland
Brownie
Phylometh
http://phylometh.info/
Brian O'Meara
Species tree
*BEAST (Heled et Drummond 2009)
BEST
BUCKy
ASTRAL
GLASS
SNAPP
*BEAST
Densitree
Bouckaert et Heled (2014)
Species tree
*BEAST (Heled et Drummond 2009)
BEST
BUCKy
ASTRAL
GLASS
SNAPP
Species validation
BP&P (Yang 2015)
GSI (Cummings 2008)
SpedeSTEM (Ence et Carstens 2011)
PHRAPL (Jackson et al. 2017)
BP&P
τ0 - čas od oddělení linií
θ - velikost populací
Analýzy
A00
A10
A01
A11
BP&P kritika
Protractedspecies model
Sukumaran et Knowles(2017)
Obhajoba BP&P
Leaché et al. (2018)
Využití metod druhové
delimitace u hub
houby X jiné organismy
(rostliny, živočichové) Willis(2017)
houby X jiné organismy
(rostliny, živočichové)
460 jedinců 2 druhy 5-7 druhů Funk et al.
(2011)
houby X jiné organismy
(rostliny, živočichové)
193 kmenů 7 druhů 21 druhů Sklenář et al.
(2017)
houby X jiné organismy
(rostliny, živočichové)
163 kmenů 22 druhů 31 druhů Chen et al.
(2017)
houby X jiné organismy
(rostliny, živočichové)
182 kmenů
7 druhů
31 druhů
Feng et al. (2016)
houby X jiné organismy
(rostliny, živočichové)
7 druhů 31 druhů 64 druhů
Taxonomie říše Fungi
Počet aktuálně akceptovaných druhů
Odhadovaný počet všech druhů hub
120 000
2 200 000 – 3 800 000
Hawksworth et Lücking (2017)
Taxonomie říše Fungi
Popsáno pouze 5 % druhů
Poměr známé a neznámé biodiverzity
Taxonomie říše Fungi
+
Rozsáhlá nepopsaná diverzita
Vývoj v posledních letech
Molekulární fylogenetika
Popis mnoha nových druhů
„species hunting“
+
Dostupnost molekulárních dat
Počet druhů hub popsaných
za rok
Data pro rok 2015 nejsou kompletní
Hawksworth et Lücking (2017)
Taxonomie a fylogeneze
rodu Aspergillus
Polyfázický druhový koncept u
rodu Aspergillus
Multilokusová fylogeneze
Morfologie
Sekundární metabolity
Fyziologie
EkologieSamson et al. (2007)
Druhové koncepty podle Zachos (2016)
Agamospeices C
Biological SC
Biosimilarity SC
Cladistic SC
Cohesion SC
Compilospecies C
Differential Fitness SC
Ecological SC
Evolutionary Significant Unit
Evolutionary SC
Genealogical SC
Genealogical Concordance SC
General Lineage SC
Genetic SC
Genic SC
Genotypic Cluster SC
Hennigian SC
Internodal SC
Least Inclusive Taxonomic Unit
Morphological SC
Non-dimensional SC
Nothospecies C
Phenetic SC
Phylogenetic SC (diagnosibility version)
Phylo-Phenetic SC
Pragmatic SC
Recognition SC
Reproductive competition SC
Successional SC
Taxonomic SC
Unified SC
Phylogenetic SC (monophyly version)
32
Druhové koncepty podle Zachos (2016)
Agamospeices C
Biological SC
Biosimilarity SC
Cladistic SC
Cohesion SC
Compilospecies C
Differential Fitness SC
Ecological SC
Evolutionary Significant Unit
Evolutionary SC
Genealogical SC
Genealogical Concordance SC
General Lineage SC
Genetic SC
Genic SC
Genotypic Cluster SC
Hennigian SC
Internodal SC
Least Inclusive Taxonomic Unit
Morphological SC
Non-dimensional SC
Nothospecies C
Phenetic SC
Phylogenetic SC (diagnosibility version)
Phylo-Phenetic SC
Pragmatic SC
Recognition SC
Reproductive competition SC
Successional SC
Taxonomic SC
Unified SC
Phylogenetic SC (monophyly version)
32
Polyfázický druhový koncept u
rodu Aspergillus
Multilokusová fylogeneze
Morfologie
Sekundární metabolity
Fyziologie
Ekologie
Genealogical concordance
phylogenetic species
recognition (GCPSR)
Taylor (2000)
Hranice
druhu
Hranice
druhu
Hranice
druhu ???
Hranice
druhu
Hranice
druhu
Konkatenace vede k
nesprávné topologii a
vysokým podporám (bs, pp)
Druhový strom Konkatenovaný strom
Degnan(2006)
Kubatko(2007)
Mendes(2017)
Genealogical concordance
phylogenetic species
recognition (GCPSR)
Taylor (2000)
Hranice
druhu
Hranice
druhu
Hranice
druhu ???
Další problémy ve fylogenezi
HGT
Hybridizace
Paralogní geny
ILS
Paralogní a
ortologní
geny v
taxonomii
Paralog β-tubulinu v taxonomii
aspergillů
Hubka et Kolařík (2012)
Hubka et Kolařík (2012)
PHYLDOG
Boussau et al.(2013)
Horizontální genový přenos(HGT)
Nekompletní třídění linií (ILS)
B – Pan paniscus
C – Pan troglodytes
H – Homo sapiens
Prüfer et al. (2012)
Příklady studií rodu
Aspergillus
Sekce Restricti podle
Peterson (2008)
7 druhů + 1 nepopsaný
Delimitace druhů v sekci
Restricti
Sklenář et al. (2017)
Polyfázický druhový koncept u
rodu Aspergillus
Multilokusová fylogeneze
Morfologie
Sekundární metabolity
Fyziologie
Ekologie
A. vitricola
A. glabripes
Růstové křivky v osmotickém gradientu
Koncentrace NaCl (% v/w)
Rych
lost rů
stu
(m
m/7
d)
Nové druhy v sekci Restricti
21 druhů
14 nově popsaných
Druhový komplex Aspergillus
viridinutans podle Barrs (2013)
CaM benA
Barrs et al. (2013)
3 nově popsané druhy
Druhový komplex
Aspergillus viridinutans
podle Sugui (2014)
Sugui et al. (2014)
Genealogical concordance
phylogenetic species
recognition (GCPSR)
Taylor (2000)
Hranice
druhu
Hranice
druhu
Hranice
druhu ???
3 nově popsané druhy
Druhový komplex
Aspergillus viridinutans
podle Sugui (2014)
Sugui et al. (2014)
Druhový komplex Aspergillus
viridinutans podle Hubka
(2018)
A. felis
A. pseudoviridinutans
A. aureolus
Druhový komplex Aspergillus
candidus
A. dobrogensis sp. nov.
Hubka et al. (2018)
„Sekce“ Versicolores
podle Peterson (2008)
4 druhy + 2 nepopsané
„Sekce“ Versicolores
podle Jurjevic (2012) a dalších
4 druhy + 2 nepopsané
17 druhů
„Section“ Versicolores
with the new methods
4 druhy + 2 nepopsané
4-5 druhů
https://itol.embl.de/
Interactive Tree of Life
4 druhy + 2 nepopsané
https://itol.embl.de/
Nové druhy v sekciNidulantes
A. tennesseensis
A. pulaauensis
A. cvjetkovicii
A. creber
A. jensenii
A. venenatus
A. sydowii
A. protuberus
A. amoenus
A. tabacinus
A. pepii
A. versicolor
A. griseoaurantiacus
A. fructus
A. hongkongensis
A. austroafricanus
A. subversicolor
A. creber
A. sydowii
A. versicolor
A. subversicolor
Versicolores
mPTP
A. westerdijkiae
A. ostianus
A. nakazawaeA. sesamicolaA. melleusA. ochraceus „1“A. onikiiA. petrakiiA. ochraceus „2“
A. cretensisAspergillus sp.A. affinisA. muricatusA. westlandensisA. auricomus
A. pseudosclerotiorum
A. bridgeriiA. subramanianiiA. freseniiA. salwaensis
A. sclerotiorum
A. persii
A. sulphureus
A. roseoglobulosus
A. neobridgeriA. ochraceopetaliformis
A. flocculosusA. insulicolaA. pulvericolaA. pseudoelegansA. occultusA. steyniiA. elegansA. robustus
Aspergillus sp. 1
Aspergillus sp. 2
Aspergillus sp. 3
Aspergillus sp. 4
Aspergillus sp. 5
Aspergillus sp. 6
Aspergillus sp. 7
Aspergillus sp. 8
Aspergillus sp. 9
Aspergillus sp. 10
Aspergillus sp. 11
Aspergillus sp. 12
Circumdati
mPTP
12 druhů vs 33
Visagie et al. (2014)
Take Home Message
Renesance druhové delimitace pokračuje
Používání metod druhové delimitace by se mělo stát standardem v taxonomii hub
Pozor na over-splitting
Seznam citacíSites Jr, JW et Jonathon C. Marshall. "Delimiting species: a Renaissance issue in systematic biology." Trends in Ecology & Evolution 18.9
(2003): 462-470.
Camargo A. "Species delimitation: a decade after the renaissance." The species problem-ongoing issues. IntechOpen, 2013.
Flot JF. "Species delimitation's coming of age." Systematic Biology 64.6 (2015): 897-899.
Zachos, FE. Species concepts in biology. Vol. 801. Cham, Switzerland: Springer, 2016.
De Queiroz K. "Species concepts and species delimitation." Systematic biology 56.6 (2007): 879-886.
Carstens BC et al. "How to fail at species delimitation." Molecular ecology 22.17 (2013): 4369-4383.
Lim GS et al. "Determining species boundaries in a world full of rarity: singletons, species delimitation methods." Systematic biology 61.1 (2011):
165-169.
Ahrens D et al. "Rarity and incomplete sampling in DNA-based species delimitation." Systematic Biology 65.3 (2016): 478-494.
Fujisawa T et Barraclough TG. 2013. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised
method and evaluation on simulated datasets. Systematic Biology. 707–724.
Reid NM et Carstens BC. 2012. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the
general mixed Yule-coalescent model. BMC Evolutionary Biology. 12:196.
Zhang J et al. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 29:2869–2876.
Jones G. 2016. Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical
Biology. 1–21.
Puillandre N et al. "ABGD, Automatic Barcode Gap Discovery for primary species delimitation." Molecular ecology 21.8 (2012): 1864-1877.
Pei, Jingwen, et al. "CLADES: A classification‐based machine learning method for species delimitation from population genetic data." Molecular ecology
resources 18.5 (2018): 1144-1156.
Heled J et Drummond A. "Bayesian inference of species trees from multilocus data." Molecular biology and evolution 27.3 (2009): 570-580.
Seznam citací
Hawksworth DL et Lücking R. "Fungal diversity revisited." (2017).
Willis SC. "One species or four? Yes!... and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of
Neotropical fishes." PloS one 12.2 (2017): e0172349.
Funk WC et al. "High levels of cryptic species diversity uncovered in Amazonian frogs." Proceedings of the Royal Society B: Biological
Sciences 279.1734 (2011): 1806-1814.
Sklenář F et al. "Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti." Studies in mycology
88 (2017): 161-236.
Chen AJ et al. "Polyphasic taxonomy of Aspergillus section Aspergillus (formerly Eurotium), and its occurrence in indoor environments and
food." Studies in mycology 88 (2017): 37-135.
Feng B et al. "Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the
Hedgehog Mushrooms (Hydnum L.)." Scientific reports 6 (2016): 25586.
Bouckaert R et Heled J. "DensiTree 2: Seeing trees through the forest." BioRxiv (2014): 012401.
Yang Z. 2015. The BPP program for species tree estimation and species delimitation. Current Zoology. 61:854–865.
Cummings MP et al. "A genealogical approach to quantifying lineage divergence." Evolution: International Journal of Organic Evolution 62.9 (2008):
2411-2422.
Ence DD et Carstens BC. "SpedeSTEM: a rapid and accurate method for species delimitation." Molecular Ecology Resources 11.3 (2011): 473-480.
Jackson ND et al. "PHRAPL: Phylogeographic inference using approximate likelihoods." Systematic Biology 66.6 (2017): 1045-1053.
Sukumaran J et Knowles LL. "Multispecies coalescent delimits structure, not species." Proceedings of the National Academy of Sciences 114.7 (2017):
1607-1612.
Leaché AD et al. "The spectre of too many species." Systematic biology 68.1 (2018): 168-181.
Samson RA et al. "The species concept in Aspergillus: recommendations of an international panel." Studies in Mycology 59 (2007): 71.
Seznam citacíTaylor JW et al. "Phylogenetic species recognition and species concepts in fungi." Fungal genetics and biology 31.1 (2000): 21-32.
Degnan JH et Rosenberg NA. "Discordance of species trees with their most likely gene trees." PLoS genetics 2.5 (2006): e68.
Kubatko LS et Degnan JH. "Inconsistency of phylogenetic estimates from concatenated data under coalescence." Systematic Biology 56.1 (2007): 17-24.
Mendes FK et Hahn MW. "Why concatenation fails near the anomaly zone." Systematic biology 67.1 (2017): 158-169.
Hubka, V, and Kolařík M. "β-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer
specificity testing and taxonomic consequences." Persoonia: Molecular Phylogeny and Evolution of Fungi 29 (2012): 1.
Prüfer, K et al. "The bonobo genome compared with the chimpanzee and human genomes." Nature 486.7404 (2012): 527.
Peterson, SW. "Phylogenetic analysis of Aspergillus species using DNA sequences from four loci." Mycologia 100.2 (2008): 205-226.
Barrs, VR et al. "Aspergillus felis sp. nov., an emerging agent of invasive aspergillosis in humans, cats, and dogs." PLoS One 8.6 (2013): e64871.
Sugui JA et al. "Genetic relatedness versus biological compatibility between Aspergillus fumigatus and related species." Journal of clinical microbiology
52.10 (2014): 3707-3721.
Hubka, V et al. "Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens
capable of interspecific hybridization." Persoonia: Molecular Phylogeny and Evolution of Fungi 41 (2018): 142.
Hubka V et al. "Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov." International
journal of systematic and evolutionary microbiology 68.4 (2018): 995-1011.
Jurjević Z et al. "Aspergillus section Versicolores: nine new species and multilocus DNA sequence based phylogeny." IMA fungus 3.1 (2012): 59-59.
Boussau B et al. "Genome-scale coestimation of species and gene trees." Genome research 23.2 (2013): 323-330.
Visagie CM et al. "Ochratoxin production and taxonomy of the yellow aspergilli (Aspergillus section Circumdati)." Studies in mycology 78 (2014): 1-61.
Zdroje obrázkůhttps://cs.wikipedia.org/wiki/Renesance#/media/File:Florence_duomo_fc01.jpg
https://slovoed.com/images/slovoed/news/400/new-logo.png?1510055386
https://palaeo-electronica.org/2000_1/retinal/images/fig17.jpg
https://uconn-today-universityofconn.netdna-ssl.com/wp-content/uploads/2014/12/densitree.jpg
http://ib.berkeley.edu/courses/ib200/2016/labs/11/coalescent_lecture.pdf
https://www.researchgate.net/profile/Baptiste_Martinet/publication/319242527/figure/fig4/AS:580476301479937@1515407743484/Species
-recognition-pairwise-matrix-Species-recognition-pairwise-matrix-based-on.png