Renesance druhové delimitace: změna druhového konceptu u ... · konceptu u rodu Aspergillus ... Taxonomie říše Fungi Počet aktuálně akceptovaných ... Renesance druhové

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


Camargo et Sites (2013)


Flot (2015)

Renesance druhové delimitace

Flot (2015)

Po

če

t člá

nků

s k

líčo

vým

slo

ve

m v

ná

zvu

Rok


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)


Agamospeices C

Biological SC

Biosimilarity SC

Cladistic SC

Cohesion SC

Compilospecies C


Ecological SC


Evolutionary SC

Genealogical SC


General Lineage SC

Genetic SC

Genic SC


Hennigian SC

Internodal SC


Morphological SC

Non-dimensional SC

Nothospecies C

Phenetic SC


Phylo-Phenetic SC

Pragmatic SC

Recognition SC


Successional SC

Taxonomic SC

Unified SC


32


Agamospeices C

Biological SC

Biosimilarity SC

Cladistic SC

Cohesion SC

Compilospecies C


Ecological SC


Evolutionary SC

Genealogical SC


General Lineage SC

Genetic SC

Genic SC


Hennigian SC

Internodal SC


Morphological SC

Non-dimensional SC

Nothospecies C

Phenetic SC


Phylo-Phenetic SC

Pragmatic SC

Recognition SC


Successional SC

Taxonomic SC

Unified SC


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


metod podle Carstens et al (2013)

Species delimitation (species hypothesis)

Species tree

Species validation546


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


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 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






STACEY (Jones 2016)


Geneland

Brownie

ABGD

Puillandre et al. (2012)






STACEY (Jones 2016)


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)


(rostliny, živočichové)

460 jedinců 2 druhy 5-7 druhů Funk et al.

(2011)



193 kmenů 7 druhů 21 druhů Sklenář et al.

(2017)



163 kmenů 22 druhů 31 druhů Chen et al.

(2017)



182 kmenů

7 druhů

31 druhů

Feng et al. (2016)



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)


Popsáno pouze 5 % druhů

Poměr známé a neznámé biodiverzity


+

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)


Agamospeices C

Biological SC

Biosimilarity SC

Cladistic SC

Cohesion SC

Compilospecies C


Ecological SC


Evolutionary SC

Genealogical SC


General Lineage SC

Genetic SC

Genic SC


Hennigian SC

Internodal SC


Morphological SC

Non-dimensional SC

Nothospecies C

Phenetic SC


Phylo-Phenetic SC

Pragmatic SC

Recognition SC


Successional SC

Taxonomic SC

Unified SC


32


Agamospeices C

Biological SC

Biosimilarity SC

Cladistic SC

Cohesion SC

Compilospecies C


Ecological SC


Evolutionary SC

Genealogical SC


General Lineage SC

Genetic SC

Genic SC


Hennigian SC

Internodal SC


Morphological SC

Non-dimensional SC

Nothospecies C

Phenetic SC


Phylo-Phenetic SC

Pragmatic SC

Recognition SC


Successional SC

Taxonomic SC

Unified SC


32


rodu Aspergillus


Morfologie


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)



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)


rodu Aspergillus


Morfologie


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)



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)


viridinutans podle Hubka

(2018)

A. felis

A. pseudoviridinutans

A. aureolus


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


17 druhů

„Section“ Versicolores

with the new methods


4-5 druhů

https://itol.embl.de/

Interactive Tree of Life


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

[email protected]

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

Documents

Renesance druhové delimitace: změna druhového konceptu u ... · konceptu u rodu Aspergillus ... Taxonomie říše Fungi Počet aktuálně akceptovaných ... Renesance druhové