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1

The phylogenetic relationships of the Andean swamp rat genus Neotomys (Rodentia, Cricetidae, Sigmodontinae) based on mitochondrial and nuclear markers

100%
Martinez J. J., Ferro L. I., Mollerach M. I., Barquez R. M.
Acta Theriologica
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2012
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tom 57
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nr 3
The aim of this study was to assess the phylogenetic position of the South American cricetid genus Neotomys using two molecular markers: one nuclear (Irbp) and one mitochondrial (mt-cyb). This genus is currently considered as incertae sedis in the Sigmodontinae radiation. The phylogenetic relationships were estimated using three approaches: Bayesian inference, maximum likelihood and parsimony. We found the genus Neotomys closely related to the genera Euneomys and Irenomys, which are also considered incertae sedis. Our results suggest a common origin for this group of genera; this fact should be reflected in the taxonomy as a supra generic group with a tribal level. However, further and deeper analysis of both molecular and morphological data are needed to diagnose and formalize the proposed tribe. The relationships of this clade to the other members of Sigmodontinae were not clear as assessed by these data sets. The three genera are distributed around the Central and Southern Andes in South America evidencing that the Andes have played an important role in the diversification of several tribes of sigmodontine rodents.
2

In search of mitochondrial markers for resolving the phylogeny of cyclophyllidean tapeworms [Platyhelminthes, Cestoda] - a test study with Davaineidae

100%
Littlewood D. T. J., Waeschenbach A., Nikolov P. N.
Acta Parasitologica
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2008
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tom 53
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nr 2
The most species rich order of tapeworms is the Cyclophyllidea and prior to wide-scale sampling of these worms for phylogenetics, we wished to develop reliable PCR primers that would capture fragments of mitochondrial (mt) DNA with phylogenetic utility across the order. Nuclear ribosomal RNA gene sequences are well-established and valuable markers for resolving flatworm interrelationships spanning a wide range of taxonomic divergences, but fail to provide resolution amongst recently diverged lineages. Entire mt genomes of selected cyclophyllidean tapeworms are available on GenBank, and we used these to design PCR primers to amplify mtDNA from cox1, rrnL and nad1 for a range of cyclophyllideans (7 davaineids, 1 hymenolepidid and 1 dilepidid) and selected outgroups (Tetrabothrius sp. and Mesocestoides sp.). A combined nuclear and mt gene data set was used to estimate a reference phylogeny and the performance of the individual genes was compared to this. Although nuclear and mt genes each contributed to the structure and stability of the phylogenetic estimate, strongest nodal support was provided by nuclear data amongst the basal lineages and by mt data amongst the most recently diverged lineages. The apparent complementarity afforded by combining nuclear and mt data was compromised by these data partitions providing conflicting signal at poorly supported nodes. Nevertheless, we argue for a combined evidence approach. PCR primers that amplify rrnL were designed and tested successfully against a diversity of cyclophyllideans; rrnL and nad1 appeared to be more informative than the fragment of cox1. The genus Raillietina was not supported by molecular evidence. The new primers will likely provide considerable resolution to estimates of cyclophyllidean interrelationships in future studies.
3
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Utility of two mitochondrial markers for identification of Picea abies refugial origin

80%
Litkowiec M., Dering M., Lewandowski A.
Dendrobiology
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2009
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tom 61
65-71
Picea abies (L.) Karst is one of the most important coniferous species of Europe from both ecological and economical points of view. Traditional methods for the gene pool conservation and biodiversity maintenance in forest ecosystems have been practiced in many countries. For progress in this field using highly polymorphic genetic molecular markers is needed. Our goal was to demonstrate the utility of two polymorphic mitochondrial markers mt15-D02 and nad1 b/c in identification native Norway spruce stands. This molecular markers were tested in 1401 individuals from 59 Polish Norway spruce populations. We detected three alleles, which are called1, 2 and3, for locus mt15-D02 and two alleles , which are called1 and2, for locus nad1 b/c in our material. All five variants of alleles indicate the natural origin of P. abies. Result of this study shows that molecular marker mt15-D02 is easy to use and more informative in compare to marker nad1 b/c.
4

Introgression of distant mitochondria into the genome of Gyrodactylus salaris: Nuclear and mitochondrial markers are necessary to identify parasite strains

70%
Zietara M. S., Rokicka M., Stojanovski S., Lumme J.
Acta Parasitologica
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2010
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tom 55
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nr 1
20-28
Novel combinations of mitochondrial DNA (CO1) and internal transcribed spacers of nuclear ribosomal DNA (ITS) were detected among Gyrodactylus parasites on brown trout (Salmo trutta L.), rainbow trout (Oncorhynchus mykiss (Walbaum)), and Ohrid trout (Salmo letnica (Karaman)) from salmonid farms in Poland and Macedonia. Some clones differed from standard ITS only by ≤ 4 nucleotides, but they belonged to a mtDNA clade that differed from the Northern European lineages of G. salaris by d MCL = 0.266 ± 0.108 (maximum composite likelihood distance). The divergence of d MCL = 0.013 ± 0.005 within the alien mtDNA clade suggested introgression from an unknown maternal ancestor into the G. salaris Malmberg genome 137 to 57 kyr ago (or, less probably, repeated introgression). A comparable modern hybrid was detected based on permanently heterozygous ITS (28 bp/1264 = 2.2%) in a clone that is widespread throughout Finnish rainbow trout farms. This was a F1 hybrid of maternal G. pomeraniae Kuusela, Ziętara et Lumme (on roach, Rutilus rutilus (L.)) and G. lavareti Malmberg (on whitefish, Coregonus lavaretus (L.)). The mtDNA of the parental species differed by d MCL = 0.290 ± 0.130. The observations emphasize that both nuclear and maternally-inherited DNA markers are necessary to characterize sexually-produced lineages or clones of Gyrodactylus. The hybridization events demonstrated predict incongruence of mitochondrial vs. nuclear gene trees, i.e., reticulate evolution in species trees.
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