TY - JOUR A1 - Baalbergen, Els A1 - Helwerda, Renate A1 - Schelfhorst, Rense A1 - Castillo Cajas, Ruth F. A1 - van Moorsel, Coline H. M. A1 - Kundrata, Robin A1 - Welter-Schultes, Francisco W. A1 - Giokas, Sinos A1 - Schilthuizen, Menno T1 - Predator-Prey Interactions between Shell-Boring Beetle Larvae and Rock-Dwelling Land Snails JF - PLOS ONE N2 - Drilus beetle larvae (Coleoptera: Elateridae) are specialized predators of land snails. Here, we describe various aspects of the predator-prey interactions between multiple Drilus species attacking multiple Albinaria (Gastropoda: Clausiliidae) species in Greece. We observe that Drilus species may be facultative or obligate Albinaria-specialists. We map geographically varying predation rates in Crete, where on average 24% of empty shells carry fatal Drilus bore holes. We also provide first-hand observations and video-footage of prey entry and exit strategies of the Drilus larvae, and evaluate the potential mutual evolutionary impacts. We find limited evidence for an effect of shell features and snail behavioral traits on inter-and intraspecifically differing predation rates. We also find that Drilus predators adjust their predation behavior based on specific shell traits of the prey. In conclusion, we suggest that, with these baseline data, this interesting predator-prey system will be available for further, detailed more evolutionary ecology studies. KW - clausiliidae KW - evolution KW - pulmonata KW - albinaria KW - behavior KW - species gastropoda Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115963 SN - 1932-6203 VL - 9 IS - 6 ER - TY - JOUR A1 - Biscotti, Maria Assunta A1 - Adolfi, Mateus Contar A1 - Barucca, Marco A1 - Forconi, Mariko A1 - Pallavicini, Alberto A1 - Gerdol, Marco A1 - Canapa, Adriana A1 - Schartl, Manfred T1 - A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths JF - Genome Biology and Evolution N2 - Gonadal sex differentiation and reproduction are the keys to the perpetuation of favorable gene combinations and positively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits shared with actinopterygians, which disappeared in the tetrapod lineage. KW - sex differentiation KW - Latimeria menadoensis KW - Protopterus annectens KW - evolution KW - testis KW - gametogenesis KW - ovary Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176774 VL - 10 IS - 6 ER - TY - JOUR A1 - Biscotti, Maria Assunta A1 - Carducci, Federica A1 - Barucca, Marco A1 - Gerdol, Marco A1 - Pallavicini, Alberto A1 - Schartl, Manfred A1 - Canapa, Adriana A1 - Contar Adolfi, Mateus T1 - The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians JF - Scientific Reports N2 - Amphibians evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution. Among amphibians, high-throughput sequencing data are very limited for Caudata, due to their largest genome sizes among terrestrial vertebrates. In this paper we present the transcriptome from the fire bellied newt Cynops orientalis. Data here presented display a high level of completeness, comparable to the fully sequenced genomes available from other amphibians. Moreover, this work focused on genes involved in gametogenesis and sexual development. Surprisingly, the gsdf gene was identified for the first time in a tetrapod species, so far known only from bony fish and basal sarcopterygians. Our analysis failed to isolate fgf24 and foxl3, supporting the possible loss of both genes in the common ancestor of Rhipidistians. In Cynops, the expression analysis of genes described to be sex-related in vertebrates singled out an expected functional role for some genes, while others displayed an unforeseen behavior, confirming the high variability of the sex-related pathway in vertebrates. KW - developmental biology KW - evolution Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-227326 VL - 10 ER - TY - JOUR A1 - Borges, Alyssa R. A1 - Link, Fabian A1 - Engstler, Markus A1 - Jones, Nicola G. T1 - The Glycosylphosphatidylinositol Anchor: A Linchpin for Cell Surface Versatility of Trypanosomatids JF - Frontiers in Cell and Developmental Biology N2 - The use of glycosylphosphatidylinositol (GPI) to anchor proteins to the cell surface is widespread among eukaryotes. The GPI-anchor is covalently attached to the C-terminus of a protein and mediates the protein’s attachment to the outer leaflet of the lipid bilayer. GPI-anchored proteins have a wide range of functions, including acting as receptors, transporters, and adhesion molecules. In unicellular eukaryotic parasites, abundantly expressed GPI-anchored proteins are major virulence factors, which support infection and survival within distinct host environments. While, for example, the variant surface glycoprotein (VSG) is the major component of the cell surface of the bloodstream form of African trypanosomes, procyclin is the most abundant protein of the procyclic form which is found in the invertebrate host, the tsetse fly vector. Trypanosoma cruzi, on the other hand, expresses a variety of GPI-anchored molecules on their cell surface, such as mucins, that interact with their hosts. The latter is also true for Leishmania, which use GPI anchors to display, amongst others, lipophosphoglycans on their surface. Clearly, GPI-anchoring is a common feature in trypanosomatids and the fact that it has been maintained throughout eukaryote evolution indicates its adaptive value. Here, we explore and discuss GPI anchors as universal evolutionary building blocks that support the great variety of surface molecules of trypanosomatids. KW - cell surface proteome KW - evolution KW - GPI-anchor KW - Kinetoplastea Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-249253 SN - 2296-634X VL - 9 ER - TY - JOUR A1 - Fiala, Brigitte A1 - Maschwitz, Ulrich T1 - Food bodies and their significance for obligate ant-association in the tree genus Macaranga (Euphorbiaceae) N2 - The production of extrafloral nectar and food bodies plays an important role in many tropical ant-plant mutualisms. In Malaysia, a close association exists between ants and some species of the pioneer tree genus Macaranga (Euphorbiaccac). Macaranga is a very diverse genus which exhibits all stages ofintcraction with ants, from facultative to obligatory associations. The ants nest inside the hollow inlcrnodes and reed mainly on food budies provided by the plants. Food body production had previously been reported only in myrrnecophytic Macaranga species, where it is usually coneentrated on protected parts or the plants such as recurved stipules. We found that non-myrmecophytic Macaranga species also produce food bodies on leaves and stems, where they are collected by a variety or ants. Levels of food body production differ between facultatively and obligatorily ant-associated species but also among the various non-myrmecophytes. This may he rdated to the degree of interaction with ants. Food body production starts at a younger age in the myrmccophytic species than in the transitional or non-myrmcccophytic Macaranga. Although food bodies of the non-inhabited Macaranga species are collected by a variety of ants, there is nu evidence of association with specific ant species. Our observations suggest that food bodies enhance the evolution of ant-plant interactions. Production of food bodies alone, however, does not appear to be the most important factor for the development of obligate myrmccopllytism in Macaranga. KW - Ant-plant interactions KW - evolution KW - food bodies KW - Macaranga KW - Malaysia KW - myrmrcophytism Y1 - 1992 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-32921 ER - TY - JOUR A1 - Floren, Andreas A1 - von Rintelen, Thomas A1 - Herbert, Paul D. N. A1 - de Araujo, Bruno Cancian A1 - Schmidt, Stefan A1 - Balke, Michael A1 - Narakusumo, Raden Pramesa A1 - Peggie, Djunijanti A1 - Ubaidillah, Rosichon A1 - von Rintelen, Kristina A1 - Müller, Tobias T1 - Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests JF - Scientific Reports N2 - Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests. KW - beta-diversity KW - community data KW - gradients KW - insects KW - hypthesis KW - evolution KW - passes KW - ants Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230565 VL - 10 ER - TY - JOUR A1 - Garcia, Tzintzuni I. A1 - Matos, Isa A1 - Shen, Yingjia A1 - Pabuwal, Vagmita A1 - Coelho, Maria Manuela A1 - Wakamatsu, Yuko A1 - Schartl, Manfred A1 - Walter, Ronald B. T1 - Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion JF - PLOS ONE N2 - Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression. KW - RNA-SEQ data KW - copy-number alteration KW - squalius alburnoides KW - gene expression KW - medaka KW - variant detection KW - transplantation KW - genome KW - generation KW - evolution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-116000 SN - 1932-6203 VL - 9 IS - 6 ER - TY - JOUR A1 - Gros, Andreas A1 - Hovestadt, Thomas A1 - Poethke, Hans Joachim T1 - Evolution of local adaptions in dispersal strategies N2 - The optimal probability and distance of dispersal largely depend on the risk to end up in unsuitable habitat. This risk is highest close to the habitat’s edge and consequently, optimal dispersal probability and distance should decline towards the habitat’s border. This selection should lead to the emergence of spatial gradients in dispersal strategies. However, gene flow caused by dispersal itself is counteracting local adaptation. Using an individual based model we investigate the evolution of local adaptations of dispersal probability and distance within a single, circular, habitat patch. We compare evolved dispersal probabilities and distances for six different dispersal kernels (two negative exponential kernels, two skewed kernels, nearest neighbour dispersal and global dispersal) in patches of different size. For all kernels a positive correlation between patch size and dispersal probability emerges. However, a minimum patch size is necessary to allow for local adaptation of dispersal strategies within patches. Beyond this minimum patch area the difference in mean dispersal distance between center and edge increases linearly with patch radius, but the intensity of local adaptation depends on the dispersal kernel. Except for global and nearest neighbour dispersal, the evolved spatial pattern are qualitatively similar for both, mean dispersal probability and distance. We conclude, that inspite of the gene-flow originating from dispersal local adaptation of dispersal strategies is possible if a habitat is of sufficient size. This presumably holds for any realistic type of dispersal kernel. KW - Ausbreitung KW - Evolution KW - Computersimulation KW - Ökologie KW - nearest-neighbour dispersal KW - global dispersal KW - evolution KW - individual based simulation Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-45406 ER - TY - JOUR A1 - Gupta, Shishir K. A1 - Minocha, Rashmi A1 - Thapa, Prithivi Jung A1 - Srivastava, Mugdha A1 - Dandekar, Thomas T1 - Role of the pangolin in origin of SARS-CoV-2: an evolutionary perspective JF - International Journal of Molecular Sciences N2 - After the recent emergence of SARS-CoV-2 infection, unanswered questions remain related to its evolutionary history, path of transmission or divergence and role of recombination. There is emerging evidence on amino acid substitutions occurring in key residues of the receptor-binding domain of the spike glycoprotein in coronavirus isolates from bat and pangolins. In this article, we summarize our current knowledge on the origin of SARS-CoV-2. We also analyze the host ACE2-interacting residues of the receptor-binding domain of spike glycoprotein in SARS-CoV-2 isolates from bats, and compare it to pangolin SARS-CoV-2 isolates collected from Guangdong province (GD Pangolin-CoV) and Guangxi autonomous regions (GX Pangolin-CoV) of South China. Based on our comparative analysis, we support the view that the Guangdong Pangolins are the intermediate hosts that adapted the SARS-CoV-2 and represented a significant evolutionary link in the path of transmission of SARS-CoV-2 virus. We also discuss the role of intermediate hosts in the origin of Omicron. KW - COVID-19 KW - SARS-CoV-2 KW - origin KW - evolution KW - intermediate host KW - pangolin KW - mutation KW - recombination KW - adaptation KW - transmission KW - comparative sequence analysis Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285995 SN - 1422-0067 VL - 23 IS - 16 ER - TY - JOUR A1 - Gupta, Shishir K. A1 - Osmanoglu, Özge A1 - Minocha, Rashmi A1 - Bandi, Sourish Reddy A1 - Bencurova, Elena A1 - Srivastava, Mugdha A1 - Dandekar, Thomas T1 - Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information JF - Frontiers in Medicine N2 - Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design. KW - T-cell epitope KW - epitope prediction KW - positive selection KW - evolution KW - immune-informatics Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-293953 SN - 2296-858X VL - 9 ER -