Bioinformatics

The Struck Lab

News

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2016 / 05/ 15

 

Asmaa arrived from Egypt visiting my lab for two years

Asmaa is finishing her PhD thesis and got a fellowship from the Egyptian government to conduct her research in my lab on polychaetes from Egypt. Welcome Asmaa and a good start in Oslo.

2015 / 12/ 01

 

Jose started his PhD position today

Welcome Jose as the first member of the Struck lab in Oslo. Jose will work on the species complex of Stygocapitella subterranea using phylogeographic and population genomic approaches.

2015 / 09 / 04

 

New position started at the Natural History Museum of UiO

At the 1st I started as a Professor of Evolutionary Genomics at the University of Oslo. I am now also Curator of the Helminth collection. Please see my new contact information below.

2015 / 07 / 23

 

Our analyses on interstitial annelids got published in Current Biology.

In these analyses we showed that the interstitial annelid grouped into groups. Given our results the interstitial realm was inhabited by two evolutionary trajectories.

2015 / 03 / 27

 

Mitochondrial genomes support monophyly of Gnathifera.

We were able to determine the first mitochondrial genomes for Gnathostomulida and Gastrotricha.

2015 / 03 / 11

 

First paper on fossils.

My first paper on a fossil is out in the Proceedings of the Royal Society. Thanks Joachim for getting me involved.

2014 / 08 / 26

 

The Heisenberg fellwoship got extended for two more years.

Good news on my own part. My fellowship was evaluated positively and I have two more years doing my research. Stay tuned.

2014 / 05 / 06

 

Two new phylogenomic paper are publishec in MBE.

We published two new papers addressing annelid and spiralian phylogeny, respectively, in MBE. Check them out.

2014/ 03 / 31

 

BaCoCa and TreSpEx manuscripts have been printed now.

Now the manuscripts discribing both programs have been printed.

2013 / 10 / 06

 

TreSpEx new version is released.

I have released now the version v1 of TreSpEx including a manual, example files and precompiled databases.

2013 / 10 / 06

 

BaCoCa new version is released.

As MPE accepted our paper on BaCoCa. We have released now the Alpha version.

2013 / 04 / 19

 

New paper about Diurodrilidae is out.

Congratulations to Anja for the paper published in MPE on the position of Diurodrilidae using mitochondrial genomes.

2013 / 02 / 11

 

Webpage is online!

Hi all, I moved my web presence to this page, so that it is more independent of my chaniging work places. It will be under construction for some time, but enjoy exploring it anyway.

Address:

 

Torsten H. Struck

Professor of Evolutionary Genomics

Curator of the Helmint collection

Department of Research and Collections

Natural History Museum

 

Postal address:

PO Box 1172 Blindern

N-0318 Oslo

Norway

 

Visiting address:

Room 209

Zoological Museum

Sars gate 1

0562 Oslo

Norway

 

phone: +47-228-51740

e-mail: t.h.struck@nhm.uio.no

A major problem in phylogenetic or phylogenomic studies is that they might be hampered by signal stemming from other process than the descent-with-modification process. Therefore, we are developing new methods to ameliorate the impact of scuh processes in phylogenetic reconstructions.

Processes such as lateral gene transfer, incomplete lineage sorting, compositional biases, mutational saturation or increased substitution rates, but also wrong assignment of a paralog to a ortholog group, so that the gene tree is inferred instead of the species, introduce artificial signal into the phylogenetic reconstruction and thus conceal the phylogenetic signal present in the dataset. Therefore, we develop new methods to determine the incongruence between different data (e.g., genes, but also morphological data) as well as some of their possible sources such as saturation, compositional biases or increased substitution rates more precisely. One such method is the PABA approach, which assesses the congruence between partitions on a node-by-node manner rather than an all or nothing approach.

In another we developed the program TreSpEx, which exploits the information present in the tree reconstruction of single gene analyses of phylogenomic datasets to detect potential paralogs or contaminations in the dataset, conduct PABA analyses in an automatic manner as well as to determine long branch and saturation indices for each taxon within the individual partition of a phylogenomic dataset. Implementations in the program are automatic BLAST searches of affected potentially paralogous sequences against selected NCBI databases to assess if a paralog was detected. With a colleague at the museum we developed the program BaCoCa, which caclulates different sequence parameters for phylogenomic datasets.

 

We bring these methods to bear on potential Long Branch problems such as might be the case with Platyzoa. The taxa grouping together as Platyzoa are characterized by strongly increased substitutions rates in molecular-phylogenetic or phylogenomic studies. However, such long-branched taxa have a tendency to artificially group together and, thus, it is uncertain if Platyzoa is a real monophyletic taxon with an overall increased substitution rate. Therefore, detection of such problems in crucial to reveal the phylogenetic signal regarding platyzoan taxa. In recent study we could convincingly show that indeed support for the monophyly of Platyzoa stemmed from artifical rather than real signal.

Phylogeny of Eunicida using four different genes. Taxa with ctenognath jaws were previously thought to be basal. Red boxes indicate nodes with conflicting signal by PABA (see Table 1 above). This tree is from Struck et al. (2006).

The influence of different strategies to analyze the data. Only using more data was not able to overwhelm the artificial signal for the monophyly of Platyzoa. Only employing sophisticated methods allowed the detection and amelioration of misleading signal resulting in the paraphyly of Platyzoa. See Struck et al. (2014).