TY  - JOUR
A1  - Hill, Natascha
A1  - Leow, Alexander
A1  - Bleidorn, Christoph
A1  - Groth, Detlef
A1  - Tiedemann, Ralph
A1  - Selbig, Joachim
A1  - Hartmann, Stefanie
T1  - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information
JF  - Theory in biosciences
N2  - 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.
KW  - Mutual Information
KW  - Evolution
KW  - Gene structure
Y1  - 2013
U6  - https://doi.org/10.1007/s12064-012-0173-0
SN  - 1431-7613
VL  - 132
IS  - 2
SP  - 93
EP  - 104
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Schröder, Christiane
A1  - Bleidorn, Christoph
A1  - Hartmann, Stefanie
A1  - Tiedemann, Ralph
T1  - Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives
N2  - 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.
Y1  - 2009
UR  - http://www.sciencedirect.com/science/journal/03781119
U6  - https://doi.org/10.1016/j.gene.2009.06.012
SN  - 0378-1119
ER  - 
TY  - JOUR
A1  - Bonizzoni, Mariangela
A1  - Bourjea, Jerome
A1  - Chen, Bin
A1  - Crain, B. J.
A1  - Cui, Liwang
A1  - Fiorentino, V.
A1  - Hartmann, Stefanie
A1  - Hendricks, S.
A1  - Ketmaier, Valerio
A1  - Ma, Xiaoguang
A1  - Muths, Delphine
A1  - Pavesi, Laura
A1  - Pfautsch, Simone
A1  - Rieger, M. A.
A1  - Santonastaso, T.
A1  - Sattabongkot, Jetsumon
A1  - Taron, C. H.
A1  - Taron, D. J.
A1  - Tiedemann, Ralph
A1  - Yan, Guiyun
A1  - Zheng, Bin
A1  - Zhong, Daibin
T1  - Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011
JF  - Molecular ecology resources
N2  - 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.
Y1  - 2011
U6  - https://doi.org/10.1111/j.1755-0998.2011.03046.x
SN  - 1755-098X
VL  - 11
IS  - 5
SP  - 935
EP  - 936
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - JOUR
A1  - Schedina, Ina-Maria
A1  - Pfautsch, Simone
A1  - Hartmann, Stefanie
A1  - Dolgener, N.
A1  - Polgar, Anika
A1  - Bianco, Pier Giorgio
A1  - Tiedemann, Ralph
A1  - Ketmaier, Valerio
T1  - Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data
JF  - Journal of fish biology
N2  - 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
KW  - conservation
KW  - population structure
KW  - species pair
Y1  - 2014
U6  - https://doi.org/10.1111/jfb.12470
SN  - 0022-1112
SN  - 1095-8649
VL  - 85
IS  - 3
SP  - 960
EP  - 964
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - Gurke, Marie
A1  - Paraskevopoulou, Sofia
A1  - Havenstein, Katja
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species
JF  - Scientific reports
N2  - Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-27137-3
SN  - 2045-2322
VL  - 12
IS  - 1
PB  - Macmillan Publishers Limited
CY  - London
ER  - 
TY  - JOUR
A1  - Cahsan, Binia De
A1  - Kiemel, Katrin
A1  - Westbury, Michael V.
A1  - Lauritsen, Maike
A1  - Autenrieth, Marijke
A1  - Gollmann, Günter
A1  - Schweiger, Silke
A1  - Stenberg, Marika
A1  - Nyström, Per
A1  - Drews, Hauke
A1  - Tiedemann, Ralph
T1  - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad
JF  - Ecology and Evolution
N2  - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.
KW  - Bombina bombina
KW  - heat shock protein
KW  - introgression
KW  - major histocompatibility complex
KW  - scaled mass index
Y1  - 2021
SN  - 2045-7758
VL  - 11
IS  - 14
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - Gurke, Marie
A1  - Paraskevopoulou, Sofia
A1  - Havenstein, Katja
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species
JF  - Scientific Reports
N2  - Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-27137-3
SN  - 2045-2322
VL  - 12
PB  - Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Mahler, B.
A1  - Schneider, A. R. R.
A1  - Di Giacomo, A. S.
A1  - Di Giacomo, A. G.
A1  - Reboreda, Juan C.
A1  - Tiedemann, Ralph
T1  - Microsatellite usefulness is independent of phylogenetic distance in Tyrant flycatchers (Aves: Tyrannidae) - a test using two globally threatened species
JF  - Genetics and molecular research
N2  - Tyrant flycatchers (Aves: Tyrannidae) are endemic to the New World, and many species of this group are threatened or near-threatened at the global level. The aim of this study was to test the 18 microsatellite markers that have been published for other Tyrant flycatchers in the Strange-tailed Tyrant (Alectrurus risora) and the Sharp-tailed Tyrant (Culicivora caudacuta), two endemic species of southern South American grasslands that are classified as vulnerable. We also analyzed the usefulness of loci in relation to phylogenetic distance to the source species. Amplification success was high in both species (77 to 83%) and did not differ between the more closely and more distantly related species to the source species. Polymorphism success was also similar for both species, with 9 and 8 loci being polymorphic, respectively. An increased phylogenetic distance thus does not gradually lead to allelic or locus dropouts, implying that in Tyrant flycatchers, the published loci are useful independent of species relatedness.
KW  - Alectrurus risora
KW  - Culicivora caudacuta
KW  - Microsatellites
KW  - Tyrannidae
Y1  - 2013
U6  - https://doi.org/10.4238/2013.August.12.12
SN  - 1676-5680
VL  - 12
IS  - 3
SP  - 2966
EP  - 2972
PB  - FUNPEC
CY  - Ribeirao Preto
ER  - 
TY  - JOUR
A1  - Foerster, Verena
A1  - Asrat, Asfawossen
A1  - Ramsey, Christopher Bronk
A1  - Brown, Erik T.
A1  - Chapot, Melissa S.
A1  - Deino, Alan
A1  - Düsing, Walter
A1  - Grove, Matthew
A1  - Hahn, Annette
A1  - Junginger, Annett
A1  - Kaboth-Bahr, Stefanie
A1  - Lane, Christine S.
A1  - Opitz, Stephan
A1  - Noren, Anders
A1  - Roberts, Helen M.
A1  - Stockhecke, Mona
A1  - Tiedemann, Ralph
A1  - Vidal, Celine M.
A1  - Vogelsang, Ralf
A1  - Cohen, Andrew S.
A1  - Lamb, Henry F.
A1  - Schaebitz, Frank
A1  - Trauth, Martin H.
T1  - Pleistocene climate variability in eastern Africa influenced hominin evolution
JF  - Nature geoscience
N2  - Despite more than half a century of hominin fossil discoveries in eastern Africa, the regional environmental context of hominin evolution and dispersal is not well established due to the lack of continuous palaeoenvironmental records from one of the proven habitats of early human populations, particularly for the Pleistocene epoch. Here we present a 620,000-year environmental record from Chew Bahir, southern Ethiopia, which is proximal to key fossil sites. Our record documents the potential influence of different episodes of climatic variability on hominin biological and cultural transformation. The appearance of high anatomical diversity in hominin groups coincides with long-lasting and relatively stable humid conditions from similar to 620,000 to 275,000 years bp (episodes 1-6), interrupted by several abrupt and extreme hydroclimate perturbations. A pattern of pronounced climatic cyclicity transformed habitats during episodes 7-9 (similar to 275,000-60,000 years bp), a crucial phase encompassing the gradual transition from Acheulean to Middle Stone Age technologies, the emergence of Homo sapiens in eastern Africa and key human social and cultural innovations. Those accumulative innovations plus the alignment of humid pulses between northeastern Africa and the eastern Mediterranean during high-frequency climate oscillations of episodes 10-12 (similar to 60,000-10,000 years bp) could have facilitated the global dispersal of H. sapiens.
KW  - Evolutionary ecology
KW  - Limnology
KW  - Palaeoclimate
Y1  - 2022
U6  - https://doi.org/10.1038/s41561-022-01032-y
SN  - 1752-0894
SN  - 1752-0908
VL  - 15
IS  - 10
SP  - 805
EP  - 811
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - De Cahsan, Binia
A1  - Nagel, Rebecca
A1  - Schedina, Ina-Maria
A1  - King, James J.
A1  - Bianco, Pier G.
A1  - Tiedemann, Ralph
A1  - Ketmaier, Valerio
T1  - Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data
JF  - Journal of fish biology
N2  - The European river lamprey Lampetra fluviatilis and the European brook lamprey Lampetra planeri (Block 1784) are classified as a paired species, characterized by notably different life histories but morphological similarities. Previous work has further shown limited genetic differentiation between these two species at the mitochondrial DNA level. Here, we expand on this previous work, which focused on lamprey species from the Iberian Peninsula in the south and mainland Europe in the north, by sequencing three mitochondrial marker regions of Lampetra individuals from five river systems in Ireland and five in southern Italy. Our results corroborate the previously identified pattern of genetic diversity for the species pair. We also show significant genetic differentiation between Irish and mainland European lamprey populations, suggesting another ichthyogeographic district distinct from those previously defined. Finally, our results stress the importance of southern Italian L. planeri populations, which maintain several private alleles and notable genetic diversity.
KW  - European lamprey
KW  - Lampetra
KW  - paired species
KW  - phylogeography
KW  - population
KW  - structure
Y1  - 2020
U6  - https://doi.org/10.1111/jfb.14279
SN  - 0022-1112
SN  - 1095-8649
VL  - 96
IS  - 4
SP  - 905
EP  - 912
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  -