@misc{ValentePhillimoreEtienne2015, author = {Valente, Luis M. and Phillimore, Albert B. and Etienne, Rampal S.}, title = {Equilibrium and non-equilibrium dynamics simultaneously operate in the Gal{\´a}pagos islands}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93525}, pages = {9}, year = {2015}, abstract = {Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Gal{\´a}pagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Gal{\´a}pagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.}, language = {en} } @phdthesis{Treplin2006, author = {Treplin, Simone}, title = {Inference of phylogenetic relationships in passerine birds (Aves: Passeriformes) using new molecular markers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-11230}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {The aim of this study was to provide deeper insights in passerine phylogenetic relationships using new molecular markers. The monophyly of the largest avian order Passeriformes (~59\% of all living birds) and the division into its suborders suboscines and oscines are well established. Phylogenetic relationships within the group have been extremely puzzling, as most of the evolutionary lineages originated through rapid radiation. Numerous studies have hypothesised conflicting passerine phylogenies and have repeatedly stimulated further research with new markers. In the present study, I used three different approaches to contribute to the ongoing phylogenetic debate in Passeriformes. I investigated the recently introduced gene ZENK for its phylogenetic utility for passerine systematics in combination and comparison to three already established nuclear markers. My phylogenetic analyses of a comprehensive data set yielded highly resolved, consistent and strongly supported trees. I was able to show the high utility of ZENK for elucidating phylogenetic relationships within Passeriformes. For the second and third approach, I used chicken repeat 1 (CR1) retrotransposons as phylogenetic markers. I presented two specific CR1 insertions as apomorphic characters, whose presence/absence pattern significantly contributed to the resolution of a particular phylogenetic uncertainty, namely the position of the rockfowl species Picathartes spp. in the passerine tree. Based on my results, I suggest a closer relationship of these birds to crows, ravens, jays, and allies. For the third approach, I showed that CR1 sequences contain phylogenetic signal and investigated their applicability in more detail. In this context, I screened for CR1 elements in different passerine birds, used sequences of several loci to construct phylogenetic trees, and evaluated their reliability. I was able to corroborate existing hypotheses and provide strong evidence for some new hypotheses, e.g. I suggest a revision of the taxa Corvidae and Corvinae as vireos are closer related to crows, ravens, and allies. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea, and Muscicapoidea was strongly supported. I found evidence for a split within Sylvioidea into two clades, one consisting of tits and the other comprising warblers, bulbuls, laughingthrushes, whitethroats, and allies. Whereas Passeridae appear to be paraphyletic, monophyly of weavers and estrild finches as a separate clade was strongly supported. The sister taxon relationships of dippers and the thrushes/flycatcher/chat assemblage was corroborated and I suggest a closer relationship of waxwings and kinglets to wrens, tree-creepers, and nuthatches.}, language = {en} } @misc{SammlerBleidornTiedemann2017, author = {Sammler, Svenja and Bleidorn, Christoph and Tiedemann, Ralph}, title = {Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400889}, pages = {10}, year = {2017}, abstract = {Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.}, language = {en} } @misc{RainfordHofreiterMayhew2016, author = {Rainford, James L. and Hofreiter, Michael and Mayhew, Peter J.}, title = {Phylogenetic analyses suggest that diversification and body size evolution are independent in insects}, series = {BMC evolutionary biology}, journal = {BMC evolutionary biology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407328}, pages = {17}, year = {2016}, abstract = {Background: Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. Results: The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Conclusions: Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.}, language = {en} } @phdthesis{Lamanna2015, author = {Lamanna, Francesco}, title = {Adaptive radiation and speciation in African weakly-electric fish}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-80097}, school = {Universit{\"a}t Potsdam}, pages = {114}, year = {2015}, abstract = {The rise of evolutionary novelties is one of the major drivers of evolutionary diversification. African weakly-electric fishes (Teleostei, Mormyridae) have undergone an outstanding adaptive radiation, putatively owing to their ability to communicate through species-specific Electric Organ Discharges (EODs) produced by a novel, muscle-derived electric organ. Indeed, such EODs might have acted as effective pre-zygotic isolation mechanisms, hence favoring ecological speciation in this group of fishes. Despite the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its ancestral counterpart, the skeletal muscle, in the genus Campylomormyrus. After having established a set of reference transcriptomes using "Next-Generation Sequencing" (NGS) technologies, I performed in silico analyses of differential expression, in order to identify sets of genes that might be responsible for the functional differences observed between these two kinds of tissues. The results of such analyses indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ; ii) the metabolic activity of the electric organ might be specialized towards the production and turnover of membrane structures; iii) several ion channels are highly expressed in the electric organ in order to increase excitability, and iv) several myogenic factors might be down-regulated by transcription repressors in the EO. A secondary task of this study is to improve the genus level phylogeny of Campylomormyrus by applying new methods of inference based on the multispecies coalescent model, in order to reduce the conflict among gene trees and to reconstruct a phylogenetic tree as closest as possible to the actual species-tree. By using 1 mitochondrial and 4 nuclear markers, I was able to resolve the phylogenetic relationships among most of the currently described Campylomormyrus species. Additionally, I applied several coalescent-based species delimitation methods, in order to test the hypothesis that putatively cryptic species, which are distinguishable only from their EOD, belong to independently evolving lineages. The results of this analysis were additionally validated by investigating patterns of diversification at 16 microsatellite loci. The results suggest the presence of a new, yet undescribed species of Campylomormyrus.}, language = {en} } @misc{FolkertsmaWestburyEccardetal.2018, author = {Folkertsma, Remco and Westbury, Michael V. and Eccard, Jana and Hofreiter, Michael}, title = {The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {481}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412994}, pages = {2}, year = {2018}, abstract = {The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.}, language = {en} }