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Partial degeneration - a solution to LBA and saturation problems
Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk systematik och evolutionsforskning. Swedish Museum of Natural History, Sweden.
Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för zoologisk systematik och evolutionsforskning. Swedish Museum of Natural History, Sweden.
(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Abstract [en]

Background: There are many factors to consider when studying evolutionary relationships. The effect of substitution saturation and compositional heterogeneity may result in erroneous relationships and long-branch attraction artifacts (LBA) are all too real for a researcher in this field. A well-used method of avoiding LBA is removal or degeneration of the faster evolving third codon positions in protein coding genes and while successful, it possibly reduces valuable information in the process. We want to test the effectiveness of degenerating synonymous sites (i.e. degen1 coding) used on only a selective part of a dataset and how it compares to the common methods otherwise used. Testing these methods, two protein coding gene datasets covering Hymenoptera and Diptera, differing in size, hierarchal level and evolutionary age, was analyzed using maximum likelihood. 

Results: Both data sets, with high support across the trees, displayed LBA in the early lineages when all codon positions were included. Both methods of dataset alteration yielded similar and more likely trees, but the partial degeneration method showed higher number of supported nodes and as well as a higher median support.

Conclusions: Partial degeneration is able to solve LBA artifacts and is a more efficient method to use when data is poorly sampled or suffers from substitution saturation and/or compositional heterogeneity. 

Nyckelord [en]
saturation, Long-branch attraction, phylogeny
Nationell ämneskategori
Biologisk systematik
Forskningsämne
zoologisk systematik och evolutionsforskning
Identifikatorer
URN: urn:nbn:se:su:diva-127993OAI: oai:DiVA.org:su-127993DiVA, id: diva2:912056
Tillgänglig från: 2016-03-15 Skapad: 2016-03-15 Senast uppdaterad: 2016-03-15Bibliografiskt granskad
Ingår i avhandling
1. Taking a Bite out of Diversity - Taxonomy and systematics of biting midges
Öppna denna publikation i ny flik eller fönster >>Taking a Bite out of Diversity - Taxonomy and systematics of biting midges
2016 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

The biting midges (family Ceratopogonidae) is one of the most species rich amongst the biting flies (Diptera) and has been recorded from most parts of the world. The species are mostly known for their capability to act as vectors for several important diseases, which have helped in shaping the focus to one of its genera, Culicoides Latreille, 1809.

 

This thesis gives an overview of the knowledge of the Swedish diversity, in the first paper (paper I) with a closer look at the species of Dasyhelea Kieffer, 1911 where all twenty species found in Sweden are presented with their associated localities, and two new species are described.  In the second paper (paper II) the biting midge diversity of Sweden is presented based on specimens collected from several localities. All these individuals were barcoded using the mitochondrial cytochrome oxidase I gene (COI). The analysis included 773 specimens that were assigned into 214 barcoding clusters (BINs) and sorted into 164 groups based on their morphology. The third paper (paper III) broadens the scale were the evolutionary relationships within the family are investigated by applying five protein coding genes (COI, CAD, TPI, AATS and PGD) and specimens from different parts of the World. The analysis recovers Ceratopogonini, Forcipomyia Meigen, 1818 and Bezzia Kieffer, 1899 as paraphyletic and Palpomyia Meigen, 1818 polyphyletic. In the last and fourth paper (paper IV) the family is used as a model organism together with Hymenoptera for an alternative analysis method for reducing the impact of saturation and long-branch attraction using non-synonymous coding (e.g. Degen1) on only parts of a dataset. The effectiveness of the method is compared to the removal of the faster evolving third codon position. The result yields a higher number of supported nodes as well as a higher median of support for the method as well as an ability to reduce long-branch attraction artifacts.

Ort, förlag, år, upplaga, sidor
Stockholm: Department of Zoology, Stockholm University, 2016. s. 28
Nyckelord
Ceratopogonidae, Dasyhelea, barcoding, COI, phylogeny Sweden, Forcipomyia, Bezzia, Palpomyia, Degen1
Nationell ämneskategori
Zoologi
Forskningsämne
zoologisk systematik och evolutionsforskning
Identifikatorer
urn:nbn:se:su:diva-127144 (URN)978-91-7649-373-1 (ISBN)
Disputation
2016-04-08, Lilla hörsalen, Naturhistoriska riksmuseet, Frescativägen 40, Stockholm, 14:00 (Engelska)
Opponent
Handledare
Forskningsfinansiär
Svenska artprojektet (ArtDatabanken, SLU), dha 157/09 1.4
Anmärkning

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.

 

Tillgänglig från: 2016-03-16 Skapad: 2016-02-26 Senast uppdaterad: 2020-04-07Bibliografiskt granskad

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Strandberg, JonasBukontaite, Rasa
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Biologisk systematik

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