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Citation for Study 26680

Citation title: "Diaporthe amygdali, a species complex or a complex species?".

Study name: "Diaporthe amygdali, a species complex or a complex species?".

This study is part of submission 26680 (Status: Published).

Citation

Hil?rio S., Santos L., & Alves A. 2021. Diaporthe amygdali, a species complex or a complex species?. Fungal Biology, .

Authors

• Hil?rio S. (submitter)
• Santos L.
• Alves A. 00351234370970

Abstract

Diaporthe represents a cosmopolitan group of fungi comprised of plant pathogens causing serious diseases on many economically important plant hosts. Therefore, an accurate identification of these pathogens is an essential step to establish adequate control measures. Nowadays, the concatenation of multilocus DNA sequences has revealed an important tool to infer phylogenetic relationships and to identify species boundaries in Diaporthe. However, the discordance between individual gene trees and the combined multilocus analysis seems to occur in the genus Diaporthe, but somehow overlooked. In this study, we noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, denominated as D. amygdali complex, occupy a monophyletic clade whose phylogenetic limits remain unclear. Therefore, to assess the boundaries of this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and the coalescent models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). Results based on these models do not support the recognition of lineages as distinct species and showed incongruent results for the concatenated gene tree. Moreover, we also showed that there are no reproductive isolation and geographical barriers to gene flow in this complex, thus, evidencing that D. amygdali complex constitutes a single species. At our knowledge, this is the first time that coalescent-based methods are implemented in the genus Diaporthe. This study provides crucial background information about the importance of coalescent methods to infer the evolutionary histories of species, and to delimitate the boundaries in the genus Diaporthe.

Keywords

Coalescent, GMYC, Phylogeny, PTP, Species delimitation, Systematics

External links

• DOI: 10.1016/j.funbio.2021.01.006
• Other URL: http://www.sciencedirect.com/science/article/pii/S1878614621000131?via%3Dihub

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S26680
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref31059,
  	 author = {Sandra  Hil?rio and Liliana  Santos and Artur  Alves},
  	 title = {Diaporthe amygdali, a species complex or a complex species?},
  	 year = {2021},
  	 keywords = {Coalescent, GMYC, Phylogeny, PTP, Species delimitation, Systematics},
  	 doi = {10.1016/j.funbio.2021.01.006},
  	 url = {http://www.sciencedirect.com/science/article/pii/S1878614621000131?via%3Dihub},
  	 pmid = {},
  	 journal = {Fungal Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Diaporthe represents a cosmopolitan group of fungi comprised of plant pathogens causing serious diseases on many economically important plant hosts. Therefore, an accurate identification of these pathogens is an essential step to establish adequate control measures. Nowadays, the concatenation of multilocus DNA sequences has revealed an important tool to infer phylogenetic relationships and to identify species boundaries in Diaporthe. However, the discordance between individual gene trees and the combined multilocus analysis seems to occur in the genus Diaporthe, but somehow overlooked. In this study, we noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, denominated as D. amygdali complex, occupy a monophyletic clade whose phylogenetic limits remain unclear. Therefore, to assess the boundaries of this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and the coalescent models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). Results based on these models do not support the recognition of lineages as distinct species and showed incongruent results for the concatenated gene tree. Moreover, we also showed that there are no reproductive isolation and geographical barriers to gene flow in this complex, thus, evidencing that D. amygdali complex constitutes a single species. At our knowledge, this is the first time that coalescent-based methods are implemented in the genus Diaporthe. This study provides crucial background information about the importance of coalescent methods to infer the evolutionary histories of species, and to delimitate the boundaries in the genus Diaporthe.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 31059
  AU  - Hil?rio,Sandra 
  AU  - Santos,Liliana 
  AU  - Alves,Artur 
  T1  - Diaporthe amygdali, a species complex or a complex species?
  PY  - 2021
  KW  - Coalescent
  KW  - GMYC
  KW  - Phylogeny
  KW  - PTP
  KW  - Species delimitation
  KW  - Systematics
  UR  - http://www.sciencedirect.com/science/article/pii/S1878614621000131?via%3Dihub
  N2  - Diaporthe represents a cosmopolitan group of fungi comprised of plant pathogens causing serious diseases on many economically important plant hosts. Therefore, an accurate identification of these pathogens is an essential step to establish adequate control measures. Nowadays, the concatenation of multilocus DNA sequences has revealed an important tool to infer phylogenetic relationships and to identify species boundaries in Diaporthe. However, the discordance between individual gene trees and the combined multilocus analysis seems to occur in the genus Diaporthe, but somehow overlooked. In this study, we noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, denominated as D. amygdali complex, occupy a monophyletic clade whose phylogenetic limits remain unclear. Therefore, to assess the boundaries of this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and the coalescent models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). Results based on these models do not support the recognition of lineages as distinct species and showed incongruent results for the concatenated gene tree. Moreover, we also showed that there are no reproductive isolation and geographical barriers to gene flow in this complex, thus, evidencing that D. amygdali complex constitutes a single species. At our knowledge, this is the first time that coalescent-based methods are implemented in the genus Diaporthe. This study provides crucial background information about the importance of coalescent methods to infer the evolutionary histories of species, and to delimitate the boundaries in the genus Diaporthe.
  L3  - 10.1016/j.funbio.2021.01.006
  JF  - Fungal Biology
  VL  - 
  IS  - 
  ER  -