Journal ArticleDOI
Species delimitation in taxonomically difficult lichen-forming fungi: an example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America.
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TLDR
The evolution of characters traditionally regarded as taxonomically important are assessed by reconstructing a phylogenetic hypothesis based on sequence data from four nuclear ribosomal markers as well as fragments from two protein-coding nuclear loci, suggesting that major diagnostic characters have evolved in a homoplasious manner.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2011-09-01. It has received 90 citations till now. The article focuses on the topics: Xanthoparmelia & Population.read more
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How to fail at species delimitation.
TL;DR: Researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
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Coalescent-based species delimitation in an integrative taxonomy
TL;DR: Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
Journal ArticleDOI
Notes for genera: Ascomycota
Nalin N. Wijayawardene,Kevin D. Hyde,Kunhiraman C. Rajeshkumar,David L. Hawksworth,Hugo Madrid,Paul M. Kirk,Uwe Braun,Rajshree V. Singh,Pedro W. Crous,Martin Kukwa,Robert Lücking,Cletus P. Kurtzman,Andrey Yurkov,Danny Haelewaters,André Aptroot,H. Thorsten Lumbsch,Einar Timdal,Damien Ertz,Javier Etayo,Alan J. L. Phillips,Johannes Z. Groenewald,Moslem Papizadeh,Laura Selbmann,Monika C. Dayarathne,Gothamie Weerakoon,E. B. Gareth Jones,Satinee Suetrong,Qing Tian,Rafael F. Castañeda-Ruiz,Ali H. Bahkali,Ka-Lai Pang,Kazuaki Tanaka,Dong-Qin Dai,Jariya Sakayaroj,Martina Hujslová,Lorenzo Lombard,Belle Damodara Shenoy,Ave Suija,Sajeewa S. N. Maharachchikumbura,Kasun M. Thambugala,Dhanushka N. Wanasinghe,Bharati O. Sharma,Subhash Gaikwad,Gargee Pandit,Laura Zucconi,Silvano Onofri,Eleonora Egidi,Huzefa A. Raja,Rampai Kodsueb,Marcela Eugenia da Silva Cáceres,Sergio Pérez-Ortega,Patrícia Oliveira Fiuza,Josiane Santana Monteiro,Larissa N. Vasilyeva,Roger G. Shivas,María Prieto,Mats Wedin,Ibai Olariaga,A. A. Lateef,Yamini Agrawal,Seyed Abolhassan Shahzadeh Fazeli,Mohammad Ali Amoozegar,Guo Zhu Zhao,Walter P. Pfliegler,Gunjan Sharma,Magdalena Oset,Mohamed A. Abdel-Wahab,Susumu Takamatsu,K. Bensch,Nimali I. de Silva,André De Kesel,Anuruddha Karunarathna,Saranyaphat Boonmee,Donald H. Pfister,Yong-Zhong Lu,Zong-Long Luo,Nattawut Boonyuen,Dinushani A. Daranagama,Indunil C. Senanayake,Subashini C. Jayasiri,Milan C. Samarakoon,Xiang-Yu Zeng,Mingkwan Doilom,Luis Quijada,Sillma Rampadarath,Gabriela Heredia,Asha J. Dissanayake,Ruvishika S. Jayawardana,Rekhani H. Perera,Li Zhou Tang,Chayanard Phukhamsakda,Margarita Hernández-Restrepo,Xiao-Ya Ma,Saowaluck Tibpromma,Luís Fernando Pascholati Gusmão,Darshani Weerahewa,Samantha C. Karunarathna +96 more
TL;DR: This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names.
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Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi
TL;DR: The role of molecular data in understanding species-level diversity in lichenized fungi is reported on by reviewing current literature, focusing primarily on Ascomycota.
Journal ArticleDOI
Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota)
Steven D. Leavitt,Ekaphan Kraichak,Matthew P. Nelsen,Susanne Altermann,Pradeep K. Divakar,David Alors,Theodore L. Esslinger,Ana Crespo,Thorsten Lumbsch +8 more
TL;DR: It is concluded that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here.
References
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Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
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MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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DnaSP v5
Pablo Librado,Julio Rozas +1 more
TL;DR: Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets, including visualizing sliding window results integrated with available genome annotations in the UCSC browser.