| 1. |
- Bengtsson, Johan, 1985, et al.
(författare)
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Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts
- 2011
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Ingår i: SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. However, the gene is not only present in the nuclear genome of eukaryotes and the core genome of prokaryotes, but also in the mitochondria and chloroplasts of eukaryotes. The SSU genes in the core genome, mitochondria and chloroplast are conceptually paralogous and should in most situations not be aligned and analyzed jointly, e.g. when estimating species diversity. Identifying the origin of SSU sequences in complex sequence datasets is a time-consuming and largely manual undertaking. To ease this situation, we have created Metaxa, an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacte- rial, nuclear eukaryote, mitochondrial, or chloroplast origin. Metaxa very efficiently detects SSU sequences from fragments as short as 200 base pairs, and correctly classifies 97% of the identified genes at read lengths typically obtained from pyrosequencing. In addition, Metaxa shows a false positive rate of 0.00012% when run on random DNA fragments, showing the robustness of the method. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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Ingår i: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
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Tidskriftsartikel (refereegranskat)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 3. |
- Karlsson, Sara, 1980, et al.
(författare)
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Social memory associated with estrogen receptor polymorphisms in women
- 2016
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Ingår i: Social Cognitive & Affective Neuroscience. - : Oxford University Press (OUP). - 1749-5016 .- 1749-5024. ; 11:6, s. 877-883
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Tidskriftsartikel (refereegranskat)abstract
- The ability to recognize the identity of faces and voices is essential for social relationships. Although the heritability of social memory is high, knowledge about the contributing genes is sparse. Since sex differences and rodent studies support an influence of estrogens and androgens on social memory, polymorphisms in the estrogen and androgen receptor genes (ESR1, ESR2, AR) are candidates for this trait. Recognition of faces and vocal sounds, separately and combined, was investigated in 490 subjects, genotyped for 10 single nucleotide polymorphisms (SNPs) in ESR1, four in ESR2 and one in the AR. Four of the associations survived correction for multiple testing: women carrying rare alleles of the three ESR2 SNPs, rs928554, rs1271572 and rs1256030, in linkage disequilibrium with each other, displayed superior face recognition compared with non-carriers. Furthermore, the uncommon genotype of the ESR1 SNP rs2504063 was associated with better recognition of identity through vocal sounds, also specifically in women. This study demonstrates evidence for associations in women between face recognition and variation in ESR2, and recognition of identity through vocal sounds and variation in ESR1. These results suggest that estrogen receptors may regulate social memory function in humans, in line with what has previously been established in mice.
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| 4. |
- Lott, Martin, et al.
(författare)
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Inferring polyploid phylogenies from multiply-labeled gene trees.
- 2009
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Ingår i: BMC evolutionary biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. RESULTS: We present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem. CONCLUSION: We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels.
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| 5. |
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| 6. |
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| 7. |
- Petri, Anna, 1980, et al.
(författare)
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Introgressive hybridization between anciently diverged lineages of Silene (Caryophyllaceae)
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization has played a major role during the evolution of angiosperms, mediating both gene flow between already distinct species and the formation of new species. Newly formed hybrids between distantly related taxa are often sterile. For this reason, interspecific crosses resulting in fertile hybrids have rarely been described to take place after more than a few million years after divergence. We describe here the traces of a reproductively successful hybrid between two ancestral species of Silene, diverged for about six million years prior to hybridization. No extant hybrids between the two parental lineages are currently known, but introgression of the RNA polymerase gene NRPA2 provides clear evidence of a temporary and fertile hybrid. Parsimony reconciliation between gene trees and the species tree, as well as consideration of clade ages, help exclude gene paralogy and lineage sorting as alternative hypotheses. This may represent one of the most extreme cases of divergence between species prior to introgressive hybridization discovered yet, notably at a homoploid level. Although species boundaries are generally believed to be stable after millions of years of divergence, we believe that this finding may indicate that gene flow between distantly related species is merely largely undetected at present.
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| 8. |
- Petri, Anna, 1980
(författare)
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Phylogenetic Inference and Allopolyploid Speciation - A Study of Silene section Physolychnis
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The major theme of this thesis is allopolyploidization, with focus on Silene section Physolychnis. The evolutionary history of an allopolyploid species can be established by inferring the sister relationships of the homoeologous sequences from low copy nuclear markers. Sequence specific primers are here used to recover co-amplified genetic variants, which is an efficient alternative to the commonly used bacterial cloning. A phylogenetic overview of Physolychnis is presented, and two major clades within the section are defined: the Asian/American clade and the Arctic/Siberian S. ajanensis group. Previously unknown ploidy levels of several taxa are inferred from sequence data, based on the number of monophyletic sequence-clusters recovered per species. Several allopolyploid taxa stemming from crosses between the two major clades are identified. Of these, S. sachalinensis and S. involucrata have indistinguishable origins, although they are geographically and morphologically distinct. Certain taxa within Physolychnis exhibit an extra copy of the nuclear gene RPA2, originating from a distantly related lineage within section Auriculatae. This is in strong conflict with the species relationships (inferred in several previous studies), and is best explained by introgression between lineages belonging to the two Silene subgenera. This finding of gene flow between such long diverged lineages may represent one of the most extreme cases presented yet. In order to investigate whether S. sachalinensis and the three subspecies of S. involucrata originate from one or several hybridization events, transcriptome data from three distantly related Silene species is used to design a set of primers for 27 loci not previously sequenced in this genus. Together with five other loci, these are amplified from 43 specimens from within the parent / allopolyploid species complex, and sequenced using 454 amplicon sequencing. This method is particularly well suited for a systematic project involving allopolyploid taxa, since sequence variants are separated on the sequencing plate, and due to the possibility of multiplexing a large number of loci and individuals. Here, a two-step PCR approach is taken to attach 10 bp barcodes to the individual amplicons. This approach is time and cost efficient, but may lead to large amounts of recombinant sequences during the second PCR amplification. Species tree inference is complicated by the presence of homoeologous gene copies within a single species. A phylogenetic tree in which identical taxon labels occur in more than one monophyletic position is here defined as a multiply labeled tree. Although several gene-trees-to-species-tree methods exist, the first consensus method that combines several multiply labeled gene trees into a multiply labeled genome tree is presented here. The genome tree can subsequently be folded into a species network, which describes the evolution of allopolyploid taxa.
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| 9. |
- Petri, Anna, 1980, et al.
(författare)
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Phylogenetic relationships within Silene (Caryophyllaceae) section Physolychnis
- 2011
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Ingår i: Taxon. - 0040-0262. ; 60:4, s. 953-968
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: Phylogenetic relationships within Silene sect. Physolychnis are investigated using DNA sequences from two low-copy nuclear regions and three plastid regions. We expand the circumscription of Physolychnis to include also Siberian and Eurasian taxa, with S. zawadzkii and S. uralensis as delimiters of the section. Two main clades are identified within Physolychnis, the Siberian S. ajanensis group and an Asian/American clade. Several taxa, previously classified to sect. Odontopetalae, sect. Occidentales, and sect. Morrisonmontanae, are shown to belong to the Asian/American clade, which otherwise corresponds to Bocquet's (1969) circumscription of sect. Physolychnis. Silene sect. Physolychnis also includes several additional, mainly Asian taxa (e.g., S. davidii, S. seoulensis, S. keiskei, S. viscosa, S. quadriloba, and homoeologues from S. songarica, S. firma, and S. tolmatchevii). Several putative allopolyploids are identified, in several cases stemming from crosses between the two main clades. The two allotetraploids S. involucrata and S. sachalinensis, although morphologically and geographically distinct, have indistinguishable ancestries.
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| 10. |
- Scheen, Anne-Cathrine, 1972, et al.
(författare)
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Use of allele-specific sequencing primers is an efficient alternative to PCR subcloning of low-copy nuclear genes
- 2012
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 12:1, s. 128-135
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Tidskriftsartikel (refereegranskat)abstract
- Direct Sanger sequencing of polymerase chain reaction (PCR)-amplified nuclear genes leads to polymorphic sequences when allelic variation is present. To overcome this problem, most researchers subclone the PCR products to separate alleles. An alternative is to directly sequence the separate alleles using allele-specific primers. We tested two methods to enhance the specificity of allele-specific primers for use in direct sequencing: using short primers and amplification refractory mutation system (ARMS) technique. By shortening the allele-specific primer to 1513 nucleotides, the single mismatch in the ultimate base of the primer is enough to hinder the amplification of the nontarget allele in direct sequencing and recover only the targeted allele at high accuracy. The deliberate addition of a second mismatch, as implemented in the ARMS technique, was less successful and seems better suited for allele-specific amplification in regular PCR rather than in direct sequencing.
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