Fungi

Comment

Comment by Kris Jett on April 23, 2012 at 7:50am

Dear Fungi group members, 

Someone has asked questions about "minimum standards for polyphasic differentiation of fungal genera" and "how many known fungal species we have and how many of them are molds?" in the Taxon-based Barcoding discussion board. I just wanted to let this group know in case any of you could provide answers.

 

Thanks so much, and keep up the good work!

Comment by Thorsten Lumbsch on July 21, 2011 at 6:34pm

Sorry - my previous comment was trunctaed. Here I try again:

 

Dear colleagues,

 

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:

1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)

2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)

In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.

If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.

What data are needed and in which format?

To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.

We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The files should be sent as combined aligned (make sure no ambiguous sites are present in the alignments) data sets in fasta format.

We will then run ML analysis for each data set separately, transform them into chronograms using Beast and run the GMYC analysis using the splits package in R.

Do not hesitate to contact me if you have any questions. We will not be able to do any analysis before the end of May for different reasons (teaching etc), but would be happy to receive data sets as soon as you have them ready.

 

Thanks a lot.

 

Cheers,

 

Thorsten

Dear colleagues,

 

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:

1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)

2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)

In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.

If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.

What data are needed and in which format?

To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.

We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The files should be sent as combined aligned (make sure no ambiguous sites are present in the alignments) data sets in fasta format.

We will then run ML analysis for each data set separately, transform them into chronograms using Beast and run the GMYC analysis using the splits package in R.

Do not hesitate to contact me if you have any questions. We will not be able to do any analysis before the end of May for different reasons (teaching etc), but would be happy to receive data sets as soon as you have them ready.

 

Thanks a lot.

 

Cheers,

 

Thorsten

Comment by Thorsten Lumbsch on July 11, 2011 at 7:02pm

Hi to all, just a short reminder that the deadline for submission of data will be coming soon (August 1, 2011) - see below.

 

Cheers,

Thorsten

 

Dear colleagues,

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:
1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)
2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)
In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.
If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.
What data are needed and in which format?
To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.
We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The f

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Comment by Pradeep Kumar Divakar on May 5, 2011 at 4:30am

Dear all,

This is a very nice idea and suggestion by Thorsten Lumbsch on species delimitation using GMYC method and good way to explore the datasets to have separate publication. Species delimitation is a crucial issue for DNA barcoding. Groups like fungi, where morphological features are scarce to delimit properly the species, correct delimitation using appropriate methodologies are prerequisite. Thus, I strongly support these coalescent based methods for species delimitation. Perhaps, it would also be good to include a method by O Meara et al. 2010. New Heuristic Methods for Joint Species Delimitation and Species Tree Inference. Syst. Biol. 59(1):59–73. A heuristic method based on coalescent model in which KC and nonparametric delimitation criteria are used.

With best regards

Divakar

 

A message from Thorsten Lumbsch to all members of Fungi on Connect.BarcodeofLife.net!

Dear colleagues,

I am suggesting to use parts of the obtained data for the barcoding paper for another analysis and separate publication. This second paper will focus on using the GMYC method to delimit species. More details on the method that has been proposed for delimitation of species and detection of cryptic species in barcoding projects, please check the following two publications:
1) Pons et al.: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects. Syst. Biol. 55: 595-609 (2006)
2) Monaghan et al.: Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation. Ssyt. Biol. 58: 298-311 (2009)
In short the method attempts at identifying a shift in branch lengths between tokogenetic (intraspecific) and phylogenetic (interspecific) relationships. We have used the method recently in different groups of lichenized ascomycetes and it seems very promising. My suggestion would be to have a paper comparing the performance of the method in a number of different fungi.
If you are interested, please submit your data until August 1, 2011 to me (tlumbsch@fieldmuseum.org). Everyone submitting data will be co-author.
What data are needed and in which format?
To make things easier for me and my colleagues, please make sure to provide the data in a form that does not require any reformatting and other extra work. Thanks a lot for your understanding.
We would need data sets with at least 2-3 samples per species and a minimum of four, closely related taxa (if you have a lot of samples per species, we can also analyze data sets with a lower number of species). Also there should be at least two loci available for all samples in the data set. The more loci, the better, but the data set should not contain missing data. Further the data set should not contain identical sequences – these should be removed before sending the files. Also make sure the names of the taxa are unique in the first eight letters of the name. The f

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