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Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to reduced insulin secretion (FFAR1 and SLC30A8), limited glycogen stores (PPP1R3E), and a unique gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2 and CTRL) and distinct pathogen diversity of blood (RNASE7) and predict the complete lack of cone-based vision in these strictly nocturnal bats (PDE6H and PDE6C). Notably, REP15 loss likely helped vampire bats adapt to high dietary iron levels by enhancing iron excretion, and the loss of CYP39A1 could have contributed to their exceptional cognitive abilities. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to blood feeding.
Im Rahmen dieser Dissertation wurden unterschiedliche Aspekte der Verbreitung der Vertreter des Pseudoterranova decipiens Komplexes betrachtet und Fragestellungen zur Ökologie und Humanpathogenität der Parasiten bearbeitet. Sie basiert auf drei (ISI-) Fachartikeln, in denen die Nutzung von Fischparasitengemeinschaften als ökologische Indikatoren für entlegene Ökosysteme des Südpolarmeeres (I), die Modellierung geeigneter Verbreitungsgebiete für Arten mit geringen Vorkommensdaten am Beispiel des P. decipiens Komplexes (II) und das Vorkommen potentiell humanpathogener P. bulbosa in unterschiedlichen Mikrohabitaten in Atlantischem Kabeljau (III) thematisiert wurde.
Die Parasitengemeinschaften der in Studie I untersuchten, nahverwandten Antarktisdorsche (Nototheniinae) Nototheniops larseni (n=40), N. nudifrons (n=40) und Lepidonotothen squamifrons (n=49) unterschieden sich hauptsächlich hinsichtlich seltener Parasitenarten. Pseudoterranova decipiens E zählte zu den häufigsten Parasiten der drei betrachteten Wirtsarten. Die Analyse der Wirtsspektren der auf Artebene bestimmten Parasiten zeigte eine geringe Spezifität antarktischer Fischparasiten im Larven- (z.B. Pseudoterranova decipiens E) und Adultstadium (z.B. Elytrophalloides oatesi). Für eine Nutzung als Bioindikatoren ergibt sich die Empfehlung, nicht auf einzelne Parasitenarten, sondern die Zusammensetzung von Parasitenfaunen zurückzugreifen und Parameter wie Abundanz oder Intensität zu berücksichtigen. Vergleiche mit Literaturdaten legten nahe, dass ein Studiendesign, das den periodischen Vergleich der Parasitierungsmuster von Nototheniinae ermöglichen soll, Standorteffekte berücksichtigen sollte. Da es sich bei der Probennahme demersaler Fische um ein aufwändiges und einschneidendes Verfahren handelt, sollten alternative Samplingmethoden vorangetrieben und eine Datenbasis dafür geschaffen werden.
Um die Belastung von Speisefischen mit potentiell humanpathogenen Parasiten in bestimmten Fanggebieten abzuschätzen, kann anhand von Vorkommens- und Umweltdaten mittels statistischer Modelle die Habitateignung für den Parasiten bestimmt werden. Eine Voraussetzung für eine verlässliche Modellierung bilden die Wahl eines geeigneten Algorithmus und die Qualität der Eingangsdaten. Für die Modellierung geeigneter Verbreitungsgebiete für die sechs Arten des P. decipiens Komplexes wurde im Rahmen von Studie II erstmalig ein biotischer Deskriptor herangezogen. Dem Ansatz lag die Annahme zugrunde, dass das Vorkommen geeigneter Endwirte der entscheidende, limitierende Faktor für die Verbreitung eines Parasiten ist, da nur so der Lebenszyklus geschlossen werden kann. Als Hypothesentest dienten Vergleiche der ökologischen Nischen von Parasiten und ihren spezifischen Endwirten im Nischenraum. Anhand der Endwirtdistanz wurde eine Verbesserung der Modellierungsergebnisse mit MaxEnt, gegenüber der ausschließlich auf abiotischen Prädiktoren basierenden Modellierung, für alle Pseudoterranova Arten, insbesondere jene mit einer geringen Anzahl Fundpunkte, erzielt. Grundsätzlich ist der Ansatz auf marine Parasitenarten, deren spezifische Endwirte verlässliche Vorkommensdaten aufweisen, übertragbar. Die Methode stellt jedoch keinen Ersatz für die Erhebung von Vorkommensdaten dar, weshalb die genetische Bestimmung schwer zu identifizierender Taxa sowie die Angabe von Metadaten in jeder parasitologischen Studie obligatorisch sein sollten.
Die Verteilung potentiell humanpathogener Parasitenstadien in für den menschlichen Verzehr vorgesehenen Fischen kann ein entscheidender Faktor für die Übertragung sein. Im Rahmen von Studie III wurde mit dem Referenztranskriptom von P. bulbosa das erste Transkriptom für eine Art den P. decipiens Komplexes erstellt. Anhand einer differentiellen Genexpressionsanalyse wurde untersucht, was die Verteilung der Parasiten auf unterschiedliche Mikrohabitate beeinflusst haben könnte. Dabei wurden siebzig differentiell exprimierte Gene identifiziert, die in aus Leber (32 Gene) und Viscera (38 Gene) von Atlantischem Kabeljau (Gadus morhua) isolierten Proben von P. bulbosa hochreguliert waren. Eine Erklärung für diesen subtilen Unterschied könnte ein Dauerstadium der P. bulbosa Larven zum Zeitpunkt der Probennahmen sein. Ob sich bestimmte Mikrohabitate innerhalb des Wirtes begünstigend auf den Parasiten auswirken, muss mit Hilfe experimenteller Studien gezeigt werden. Erste in Studie III erhobene Daten zum allergenen Potential von P. bulbosa sollten in serologischen Studien getestet werden. Als Grundlage für die Bewertung des pathogenen Potentials von P. bulbosa, sowie der weiteren Arten des P. decipiens Komplexes, sollten in experimentellen Studien NGS-Daten erhoben werden.
Im Rahmen dieser Dissertation wurde in drei methodisch unterschiedlichen Studien ein Bedarf besserer Referenzdaten aufgezeigt. Bestreben diese Datenlücken zu schließen, um das Potential der Methoden besser ausschöpfen zu können, müssen zukünftig noch weiter verstärkt werden.
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.
Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.
Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.
Climate change is influencing some environmental variables in the Southern Ocean (SO) and this will have an effect on the marine biodiversity. Peracarid crustaceans are one of the dominant and most species-rich groups of the SO benthos. To date, our knowledge on the influence of environmental variables in shaping abundance and species composition in the SO’s peracarid assemblages is limited, and with regard to ice coverage it is unknown. The aim of our study was to assess the influence of sea ice coverage, chlorophyll-a, and phytoplankton concentrations on abundance, distribution and assemblage structure of peracarids. In addition, the influence of other physical parameters on peracarid abundance was assessed, including depth, temperature, salinity, sediment type, current velocity, oxygen, iron, nitrate, silicate and phosphate. Peracarids were sampled with an epibenthic sledge (EBS) in different areas of the Atlantic sector of the SO and in the Weddell Sea. Sampling areas were characterized by different regimes of ice coverage (the ice free South Orkney Islands, the seasonally ice-covered Filchner Trough and the Eastern Antarctic Peninsula including the Prince Gustav Channel which was formerly covered by a perennial ice shelf). In total 64766 individuals of peracarids were collected and identified to order level including five orders: Amphipoda, Cumacea, Isopoda, Mysidacea, and Tanaidacea. Amphipoda was the most abundant taxon, representing 32% of the overall abundances, followed by Cumacea (31%), Isopoda (29%), Mysidacea (4%), and Tanaidacea (4%). The Filchner Trough had the highest abundance of peracarids, while the South Orkney Islands showed the lowest abundance compared to other areas. Ice coverage was the main environmental driver shaping the abundance pattern and assemblage structure of peracarids and the latter were positively correlated with ice coverage and chlorophyll-a concentration. We propose that the positive correlation between sea ice and peracarid abundances is likely due to phytoplankton blooms triggered by seasonal sea ice melting, which might increase the food availability for benthos. Variations in ice coverage extent and seasonality due to climate change would strongly influence the abundance and assemblage structure of benthic peracarids.
Peronospora salviae‐officinalis, the causal agent of downy mildew on common sage, is an obligate biotrophic pathogen. It grows in the intercellular spaces of the leaf tissue of sage and forms intracellular haustoria to interface with host cells. Although P. salviae‐officinalis was described as a species of its own 10 years ago, the infection process remains obscure. To address this, a histological study of various infection events, from the adhesion of conidia on the leaf surface to de novo sporulation is presented here. As histological studies of oomycetes are challenging due to the lack of chitin in their cell wall, we also present an improved method for staining downy mildews for confocal laser scanning microscopy as well as evaluating the potential of autofluorescence of fixed nonstained samples. For staining, a 1:1 mixture of aniline blue and trypan blue was found most suitable and was used for staining of oomycete and plant structures, allowing discrimination between them as well as the visualization of plant immune responses. The method was also used to examine samples of Peronospora lamii on Lamium purpureum and Peronospora belbahrii on Ocimum basilicum, demonstrating the potential of the presented histological method for studying the infection processes of downy mildews in general.
Schistosomiasis is a severe neglected tropical disease caused by trematodes and transmitted by freshwater snails. Snails are known to be highly tolerant to agricultural pesticides. However, little attention has been paid to the ecological consequences of pesticide pollution in areas endemic for schistosomiasis, where people live in close contact with non-sanitized freshwaters. In complementary laboratory and field studies on Kenyan inland areas along Lake Victoria, we show that pesticide pollution is a major driver in increasing the occurrence of host snails and thus the risk of schistosomiasis transmission. In the laboratory, snails showed higher insecticide tolerance to commonly found pesticides than associated invertebrates, in particular to the neonicotinoid Imidacloprid and the organophosphate Diazinon. In the field, we demonstrated at 48 sites that snails were present exclusively in habitats characterized by pesticide pollution and eutrophication. Our analysis revealed that insensitive snails dominated over their less tolerant competitors. The study shows for the first time that in the field, pesticide concentrations considered “safe” in environmental risk assessment have indirect effects on human health. Thus we conclude there is a need for rethinking the environmental risk of low pesticide concentrations and of integrating agricultural mitigation measures in the control of schistosomiasis.
Currently, the genus Polypedates comprises 26 species distributed in South, Southeast, and East Asia. Because of their relatively low dispersal capability and intolerance to seawater, this genus is ideal for the study of terrestrial range evolution that extends into the island archipelagos of southeastern Asia. In this study, based on data compiled for Polypedates from previous studies and partial mitochondrial and nuclear genes collected in this study, we performed systematic biogeographical analysis. We confirmed a Sundaland origin for the extant genus and showed northward dispersal into mainland Southeast Asia and Asia, which coincided with the timing of paleoclimatic change from the Oligocene to Middle Miocene. Climate fluctuations had a profound impact on species diversification within the genus Polypedates. Furthermore, the Red River did not mediate species exchange between Southeast Asia and mainland Asia until the end of the Miocene, with the sudden onset of northward dispersal in several clades independently at that time. Alternatively, the lineage of widespread insular P. leucomystax strongly supports the hypothesis of terrestrial connection between island archipelagos of Southeast Asia during the Mid-Pleistocene paleoclimate fluctuations. Our biogeographical analysis also supports the recent introduction of P. leucomystax to the Philippines and Ryukyus, as previously suggested.
The oomycete genus Ectrogella currently comprises a rather heterogeneous group of obligate endoparasitoids, mostly of diatoms and algae. Despite their widespread occurrence, little is known regarding the phylogenetic affinities of these bizarre organisms. Traditionally, the genus was included within the Saprolegniales, based on zoospore diplanetism and a saprolegnia/achlya-like zoospore discharge. The genus has undergone multiple re-definitions in the past, and has often been used largely indiscriminately for oomycetes forming sausage-like thalli in diatoms. While the phylogenetic affinity of the polyphyletic genus Olpidiopsis has recently been partially resolved, taxonomic placement of the genus Ectrogella remained unresolved, as no sequence data were available for species of this genus. In this study, we report the phylogenetic placement of Ectrogella bacillariacearum infecting the freshwater diatom Nitzschia sigmoidea. The phylogenetic reconstruction shows that Ectrogella bacillariacearum is grouped among the early diverging lineages of the Saprolegniomycetes with high support, and is unrelated to the monophyletic diatom-infecting olpidiopsis-like species. As these species are neither related to Ectrogella, nor to the early diverging lineages of Olpidiopsis s. str. and Miracula, they are placed in a new genus, Diatomophthora, in the present study.