@article{SpoererLenkeitBosseetal.2020,
  author    = {Sp{\"o}rer, Nadine and Lenkeit, Jenny and Bosse, Stefanie and Hartmann, Anne and Ehlert, Antje and Knigge, Michel},
  title     = {Students' perspective on inclusion},
  series = {International journal of educational research},
  volume    = {103},
  journal   = {International journal of educational research},
  publisher = {Elsevier Science},
  address   = {Oxford},
  issn      = {0883-0355},
  doi       = {10.1016/j.ijer.2020.101641},
  pages     = {13},
  year      = {2020},
  abstract  = {The goal of the present study was to analyze how students' attitudes towards inclusive education develop over the course of a school year and how these attitudes relate to students' peer relations. Sixth- and seventh-graders of 44 inclusive classes filled out a questionnaire at two measurement points within one school year to assess attitudes towards inclusive education and peer relations. Applying multilevel regression analyses it turned out that changes in peer relations over time were positively predicted by students' attitudes towards instructional adaptations for students with behaviour difficulties. Further, students with self-perceived behavior difficulties reported lower scores for peer relations compared to students without self-perceived difficulties. Results are discussed with respect to structural factors and individual characteristics affecting inclusive education.},
  language  = {en}
}
@article{ChengHartmannGuptaetal.2009,
  author    = {Cheng, Fuxia and Hartmann, Stefanie and Gupta, Mayetri and Ibrahim, Joseph G. and Vision, Todd J.},
  title     = {A hierarchical model for incomplete alignments in phylogenetic inference},
  issn      = {1367-4803},
  doi       = {10.1093/bioinformatics/btp015},
  year      = {2009},
  abstract  = {Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies. Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a pro. le likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family.},
  language  = {en}
}
@article{DennisBallesterosRobinetal.2020,
  author    = {Dennis, Alice B. and Ballesteros, Gabriel I. and Robin, St{\´e}phanie and Schrader, Lukas and Bast, Jens and Bergh{\"o}fer, Jan and Beukeboom, Leo W. and Belghazi, Maya and Bretaudeau, Anthony and Buellesbach, Jan and Cash, Elizabeth and Colinet, Dominique and Dumas, Zo{\´e} and Errbii, Mohammed and Falabella, Patrizia and Gatti, Jean-Luc and Geuverink, Elzemiek and Gibson, Joshua D. and Hertaeg, Corinne and Hartmann, Stefanie and Jacquin-Joly, Emmanuelle and Lammers, Mark and Lavandero, Blas I. and Lindenbaum, Ina and Massardier-Galata, Lauriane and Meslin, Camille and Montagn{\´e}, Nicolas and Pak, Nina and Poiri{\´e}, Maryl{\`e}ne and Salvia, Rosanna and Smith, Chris R. and Tagu, Denis and Tares, Sophie and Vogel, Heiko and Schwander, Tanja and Simon, Jean-Christophe and Figueroa, Christian C. and Vorburger, Christoph and Legeai, Fabrice and Gadau, J{\"u}rgen},
  title     = {Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum},
  series = {BMC Genomics},
  volume    = {21},
  journal   = {BMC Genomics},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-020-6764-0},
  pages     = {27},
  year      = {2020},
  abstract  = {Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8\%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.},
  language  = {en}
}
@article{HilgersHartmannHofreiteretal.2018,
  author    = {Hilgers, Leon and Hartmann, Stefanie and Hofreiter, Michael and von Rintelen, Thomas},
  title     = {Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation},
  series = {Molecular biology and evolution},
  volume    = {35},
  journal   = {Molecular biology and evolution},
  number    = {7},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msy052},
  pages     = {1638 -- 1652},
  year      = {2018},
  abstract  = {The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.},
  language  = {en}
}
@article{LahLoeberHsiangetal.2017,
  author    = {Lah, Ljerka and L{\"o}ber, Ulrike and Hsiang, Tom and Hartmann, Stefanie},
  title     = {A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles},
  series = {Fungal biology},
  volume    = {121},
  journal   = {Fungal biology},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1878-6146},
  doi       = {10.1016/j.funbio.2016.12.002},
  pages     = {234 -- 252},
  year      = {2017},
  abstract  = {Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.},
  language  = {en}
}
@article{HofreiterHartmann2020,
  author    = {Hofreiter, Michael and Hartmann, Stefanie},
  title     = {Reconstructing protein-coding sequences from ancient DNA},
  series = {Odorant binding and chemosensory proteins},
  volume    = {642},
  journal   = {Odorant binding and chemosensory proteins},
  publisher = {Academic Press, an imprint of Elsevier},
  address   = {Cambridge, MA.},
  isbn      = {978-0-12-821157-1},
  issn      = {0076-6879},
  doi       = {10.1016/bs.mie.2020.05.008},
  pages     = {21 -- 33},
  year      = {2020},
  abstract  = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.},
  language  = {en}
}
@article{WestburyBalekaBarlowetal.2017,
  author    = {Westbury, Michael V. and Baleka, Sina Isabelle and Barlow, Axel and Hartmann, Stefanie and Paijmans, Johanna L. A. and Kramarz, Alejandro and Forasiepi, Analia M. and Bond, Mariano and Gelfo, Javier N. and Reguero, Marcelo A. and Lopez-Mendoza, Patricio and Taglioretti, Matias and Scaglia, Fernando and Rinderknecht, Andres and Jones, Washington and Mena, Francisco and Billet, Guillaume and de Muizon, Christian and Luis Aguilar, Jose and MacPhee, Ross D. E. and Hofreiter, Michael},
  title     = {A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica},
  series = {Nature Communications},
  volume    = {8},
  journal   = {Nature Communications},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/ncomms15951},
  pages     = {8},
  year      = {2017},
  abstract  = {The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95\% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.},
  language  = {en}
}
@article{AutenriethHartmannLahetal.2018,
  author    = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph},
  title     = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12932},
  pages     = {1469 -- 1481},
  year      = {2018},
  abstract  = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.},
  language  = {en}
}
@article{ParaskevopoulouDennisWeithoffetal.2019,
  author    = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Hartmann, Stefanie and Tiedemann, Ralph},
  title     = {Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto},
  series = {PLoS ONE},
  volume    = {9},
  journal   = {PLoS ONE},
  number    = {14},
  publisher = {PLoS ONE},
  address   = {San Francisco, California},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0223134},
  pages     = {21},
  year      = {2019},
  abstract  = {Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).},
  language  = {en}
}
@article{HartmannPreickAbeltetal.2020,
  author    = {Hartmann, Stefanie and Preick, Michaela and Abelt, Silke and Scheffel, Andr{\´e} and Hofreiter, Michael},
  title     = {Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea},
  series = {BMC Research Notes},
  volume    = {13},
  journal   = {BMC Research Notes},
  publisher = {Biomed Central},
  address   = {London},
  issn      = {1756-0500},
  doi       = {10.1186/s13104-020-05254-4},
  pages     = {6},
  year      = {2020},
  abstract  = {Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira's lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2\% and 89.5\%, respectively. We used their predicted genes together with publicly available data from other Ericales' genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.},
  language  = {en}
}
@article{BarlowHartmannGonzalezetal.2020,
  author    = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Consensify},
  series = {Genes / Molecular Diversity Preservation International},
  volume    = {11},
  journal   = {Genes / Molecular Diversity Preservation International},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes11010050},
  pages     = {22},
  year      = {2020},
  abstract  = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.},
  language  = {en}
}
@article{StruckPaulHilletal.2011,
  author    = {Struck, Torsten H. and Paul, Christiane and Hill, Natascha and Hartmann, Stefanie and Hoesel, Christoph and Kube, Michael and Lieb, Bernhard and Meyer, Achim and Tiedemann, Ralph and Purschke, Guenter and Bleidorn, Christoph},
  title     = {Phylogenomic analyses unravel annelid evolution},
  series = {Nature : the international weekly journal of science},
  volume    = {471},
  journal   = {Nature : the international weekly journal of science},
  number    = {7336},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {0028-0836},
  doi       = {10.1038/nature09864},
  pages     = {95 -- U113},
  year      = {2011},
  abstract  = {Annelida, the ringed worms, is a highly diverse animal phylum that includes more than 15,000 described species and constitutes the dominant benthic macrofauna from the intertidal zone down to the deep sea. A robust annelid phylogeny would shape our understanding of animal body-plan evolution and shed light on the bilaterian ground pattern. Traditionally, Annelida has been split into two major groups: Clitellata (earthworms and leeches) and polychaetes (bristle worms), but recent evidence suggests that other taxa that were once considered to be separate phyla (Sipuncula, Echiura and Siboglinidae (also known as Pogonophora)) should be included in Annelida(1-4). However, the deep-level evolutionary relationships of Annelida are still poorly understood, and a robust reconstruction of annelid evolutionary history is needed. Here we show that phylogenomic analyses of 34 annelid taxa, using 47,953 amino acid positions, recovered a well-supported phylogeny with strong support for major splits. Our results recover chaetopterids, myzostomids and sipunculids in the basal part of the tree, although the position of Myzostomida remains uncertain owing to its long branch. The remaining taxa are split into two clades: Errantia (which includes the model annelid Platynereis), and Sedentaria (which includes Clitellata). Ancestral character trait reconstructions indicate that these clades show adaptation to either an errant or a sedentary lifestyle, with alteration of accompanying morphological traits such as peristaltic movement, parapodia and sensory perception. Finally, life history characters in Annelida seem to be phylogenetically informative.},
  language  = {en}
}
@article{HartmannHelmNickeletal.2012,
  author    = {Hartmann, Stefanie and Helm, Conrad and Nickel, Birgit and Meyer, Matthias and Struck, Torsten H. and Tiedemann, Ralph and Selbig, Joachim and Bleidorn, Christoph},
  title     = {Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data},
  series = {PLoS one},
  volume    = {7},
  journal   = {PLoS one},
  number    = {1},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0029843},
  pages     = {8},
  year      = {2012},
  abstract  = {Background: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic ( or parasitic) protostomes that are either placed with annelids or flatworms. Methodology: Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions: Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.},
  language  = {en}
}
@article{HillLeowBleidornetal.2013,
  author    = {Hill, Natascha and Leow, Alexander and Bleidorn, Christoph and Groth, Detlef and Tiedemann, Ralph and Selbig, Joachim and Hartmann, Stefanie},
  title     = {Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information},
  series = {Theory in biosciences},
  volume    = {132},
  journal   = {Theory in biosciences},
  number    = {2},
  publisher = {Springer},
  address   = {New York},
  issn      = {1431-7613},
  doi       = {10.1007/s12064-012-0173-0},
  pages     = {93 -- 104},
  year      = {2013},
  abstract  = {Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.},
  language  = {en}
}
@article{BurleighBansalEulensteinetal.2011,
  author    = {Burleigh, J. Gordon and Bansal, Mukul S. and Eulenstein, Oliver and Hartmann, Stefanie and Wehe, Andre and Vision, Todd J.},
  title     = {Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees},
  series = {Systematic biology},
  volume    = {60},
  journal   = {Systematic biology},
  number    = {2},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1063-5157},
  doi       = {10.1093/sysbio/syq072},
  pages     = {117 -- 125},
  year      = {2011},
  abstract  = {Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.},
  language  = {en}
}
@article{SchroederBleidornHartmannetal.2009,
  author    = {Schr{\"o}der, Christiane and Bleidorn, Christoph and Hartmann, Stefanie and Tiedemann, Ralph},
  title     = {Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives},
  issn      = {0378-1119},
  doi       = {10.1016/j.gene.2009.06.012},
  year      = {2009},
  abstract  = {Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98\%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (doglike carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony- informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.},
  language  = {en}
}
@article{BartelHartmannLehmannetal.2012,
  author    = {Bartel, Manuela and Hartmann, Stefanie and Lehmann, Karola and Postel, Kai and Quesada, Humberto and Philipp, Eva E. R. and Heilmann, Katja and Micheel, Burkhard and Stuckas, Heiko},
  title     = {Identification of sperm proteins as candidate biomarkers for the analysis of reproductive isolation in Mytilus: a case study for the enkurin locus},
  series = {Marine biology : international journal on life in oceans and coastal waters},
  volume    = {159},
  journal   = {Marine biology : international journal on life in oceans and coastal waters},
  number    = {10},
  publisher = {Springer},
  address   = {New York},
  issn      = {0025-3162},
  doi       = {10.1007/s00227-012-2005-7},
  pages     = {2195 -- 2207},
  year      = {2012},
  abstract  = {Sperm proteins of the marine sessile mussels of the Mytilus edulis species complex are models to investigate reproductive isolation and speciation. This study aimed at identifying sperm proteins and their corresponding genes. This was aided by the use of monoclonal antibodies that preferentially bind to yet unknown sperm molecules. By identifying their target molecules, this approach identified proteins with relevance to Mytilus sperm function. This procedure identified 16 proteins, for example, enkurin, laminin, porin and heat shock proteins. The potential use of these proteins as genetic markers to study reproductive isolation is exemplified by analysing the enkurin locus. Enkurin evolution is driven by purifying selection, the locus displays high levels of intraspecific variation and species-specific alleles group in distinct phylogenetic clusters. These findings characterize enkurin as informative candidate biomarker for analyses of clinal variation and differential introgression in hybrid zones, for example, to understand determinants of reproductive isolation in Baltic Mytilus populations.},
  language  = {en}
}
@article{BonizzoniBourjeaChenetal.2011,
  author    = {Bonizzoni, Mariangela and Bourjea, Jerome and Chen, Bin and Crain, B. J. and Cui, Liwang and Fiorentino, V. and Hartmann, Stefanie and Hendricks, S. and Ketmaier, Valerio and Ma, Xiaoguang and Muths, Delphine and Pavesi, Laura and Pfautsch, Simone and Rieger, M. A. and Santonastaso, T. and Sattabongkot, Jetsumon and Taron, C. H. and Taron, D. J. and Tiedemann, Ralph and Yan, Guiyun and Zheng, Bin and Zhong, Daibin},
  title     = {Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011},
  series = {Molecular ecology resources},
  volume    = {11},
  journal   = {Molecular ecology resources},
  number    = {5},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  organization    = {Mol Ecology Resources Primer Dev},
  issn      = {1755-098X},
  doi       = {10.1111/j.1755-0998.2011.03046.x},
  pages     = {935 -- 936},
  year      = {2011},
  abstract  = {This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.},
  language  = {en}
}
@article{SchedinaPfautschHartmannetal.2014,
  author    = {Schedina, Ina-Maria and Pfautsch, Simone and Hartmann, Stefanie and Dolgener, N. and Polgar, Anika and Bianco, Pier Giorgio and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data},
  series = {Journal of fish biology},
  volume    = {85},
  journal   = {Journal of fish biology},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0022-1112},
  doi       = {10.1111/jfb.12470},
  pages     = {960 -- 964},
  year      = {2014},
  abstract  = {Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0.388 and 0.424 and a mean observed heterozygosity of 0.418 and 0.411, respectively. (C) 2014 The Fisheries Society of the British Isles},
  language  = {en}
}
@article{ZulawskiSchulzeBraginetsetal.2014,
  author    = {Zulawski, Monika and Schulze, Gunnar and Braginets, Rostyslav and Hartmann, Stefanie and Schulze, Waltraud X.},
  title     = {The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification},
  series = {BMC genomics},
  volume    = {15},
  journal   = {BMC genomics},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/1471-2164-15-548},
  pages     = {14},
  year      = {2014},
  abstract  = {Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.},
  language  = {en}
}