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Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on X-ray microfocus sources (X-μCT) and Synchrotron Radiation (SR-μCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through high-resolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossilization, X-ray analyses of tooth tissues do not always provide distinct imaging contrasts, thus preventing the extraction of essential morphological and anatomical details. We illustrate here by three examples the successful application of neutron microtomography (n-μCT) in cases where X-rays have previously failed to deliver contrasts between dental tissues of fossilized specimen.
Phylogenetic analyses of nuclear and mitochondrial genomes indicate that polar bears captured the brown bear mitochondrial genome 160,000 years ago, leading to an extinction of the original polar bear mitochondrial genome. However, mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochondrial integrations). Screening the polar bear genome identified only 13 numts. Genomic analyses of two additional ursine bears and giant panda indicate that all except one of the discovered numts entered the bear lineage at least 14 million years ago. However, short read genome assemblies might lead to an under-representation of numts or other repetitive sequences. Our findings suggest low integration rates of numts in bears and a loss of the original polar bear mitochondrial genome.
Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
Morphological malformations induced by tributyltin (TBT) exposure during embryonic development have already been characterized in various taxonomic groups, but, nonetheless, the molecular processes underlying these changes remain obscure. The present study provides the first genome-wide screening for differentially expressed genes that are linked to morphological alterations of gonadal tissue from chicken embryos after exposure to TBT. We applied a single injection of TBT (between 0.5 and 30 pg as Sn/g egg) into incubated fertile eggs to simulate maternal transfer of the endocrine disruptive compound. Methyltestosterone (MT) served as a positive control (30 pg/g egg). After 19 days of incubation, structural features of the gonads as well as genome-wide gene expression profiles were assessed simultaneously. TBT induced significant morphological and histological malformations of gonadal tissue from female embryos that show a virilization of the ovaries. This phenotypical virilization was mirrored by altered expression profiles of sex-dependent genes. Among these are several transcription and growth factors (e.g. FGF12, CTCF, NFIB), whose altered expression might serve as a set of markers for early identification of endocrine active chemicals that affect embryonic development by transcriptome profiling without the need of elaborate histological analyses.
Solenogastres (Aplacophora) is a small clade of marine, shell-less worm-molluscs with close to 300 valid species. Their distribution ranges across all oceans, and whereas the vast majority of species has been collected and described from the continental shelf and slope, only few species are known from depths below 4,000 m. Following traditional taxonomy, identification of specimens to species level is complex and time-consuming and requires detailed investigations of morphology and anatomy—often resulting in the exclusion of the clade in biodiversity or biogeographic studies. During the KuramBio expedition (Kuril-Kamchatka Biodiversity Studies) to the abyssal plain of the Northwest Pacific and the Kuril-Kamchatka Trench, 33 solenogaster specimens were sampled from 4,830 m to 5,397 m. Within this study we present an efficient workflow to address solenogaster diversity, even when confronted with a high degree of singletons and minute body sizes, hampering the use of single individuals for multiple morphological and molecular approaches. We combine analyses of external characters and scleritome with molecular barcoding based on a self-designed solenogaster specific set of mitochondrial primers. Overall we were able to delineate at least 19 solenogaster lineages and identify 15 species to family level and beyond. Based on our approach we identified three key lineages from the two regionally most species-rich families (Acanthomeniidae and Pruvotinidae) for deeper taxonomic investigations and describe the novel abyssal species Amboherpia abyssokurilensis sp. nov. (Cavibelonia, Acanthomeniidae) using microanatomical 3D-reconstructions. Our study more than doubles the previous records of solenogaster species from the Northwest Pacific and its marginal seas. Almost all lineages are reported for the first time from the region of the (Northwest) Pacific, vastly expanding distribution ranges of the respective clades. Moreover it doubles the number of Solenogastres collected from abyssal depths on a global scale and underlines the lack of exploratory α-diversity work in the abyssal zone for reliable species estimates in marine biodiversity.
Feeding type and development drive the ingestion of microplastics by freshwater invertebrates
(2017)
Microscopic plastic items (microplastics) are ubiquitously present in aquatic ecosystems. With decreasing size their availability and potential to accumulate throughout food webs increase. However, little is known on the uptake of microplastics by freshwater invertebrates. To address this, we exposed species with different feeding strategies to 1, 10 and 90 µm fluorescent polystyrene spheres (3–3 000 particles mL−1). Additionally, we investigated how developmental stages and a co-exposure to natural particles (e.g., food) modulate microplastic ingestion. All species ingested microplastics in a concentration-dependent manner with Daphnia magna consuming up to 6 180 particles h−1, followed by Chironomus riparius (226 particles h−1), Physella acuta (118 particles h−1), Gammarus pulex (10 particles h−1) and Lumbriculus variegatus (8 particles h−1). D. magna did not ingest 90 µm microplastics whereas the other species preferred larger microplastics over 1 µm in size. In C. riparius and D. magna, size preference depended on the life stage with larger specimens ingesting more and larger microplastics. The presence of natural particles generally reduced the microplastics uptake. Our results demonstrate that freshwater invertebrates have the capacity to ingest microplastics. However, the quantity of uptake depends on their feeding type and morphology as well as on the availability of microplastics.
Phytotoxic dioxolanones from Guignardia bidwellii can be described as potential virulence factors which cause the formation of lesions upon an infection by G. bidwellii. The toxin guignardic acid was found in planta of G. bidwellii-infected Vitis vinifera leaves, whereas no phytotoxic dioxolanones were detected in uninfected leaf material. Secondary metabolism analyses of further phytopathogenic fungi from the genus Guignardia led to the observation that all species investigated can produce the phytotoxins known from G. bidwellii. In addition to these studies, it was demonstrated that phenguignardic acid is biosynthetically derived from two molecules of phenylalanine and that phenylalanine is a key precursor in the biosynthesis of the two other phytotoxins – alaguignardic acid and guignardic acid.
A considerable body of the literature considers the potential impact of exotic predators on native prey organisms, while comparatively, few studies have asked whether and how native predators include novel prey types into their diet spectrum. Here, we asked whether the native aquatic heteropteran Diplonychus esakii preys on the highly invasive western mosquitofish (Gambusia affinis), which has been introduced to southern China and threatens native fish species through competition and predation on their fry. We conducted 48-h prey choice experiments under semi-natural conditions. In a ‘no-choice’ experiment (one predator and one potential prey; n = 200), we found the heteropterans to prey more on large-bodied fish, a pattern that was also described for other belostomatids, while prey sex had no effect on capture rates. Moreover, large-bodied heteropterans caught more fish than small-bodied individuals. However, overall capture rates in our study were low (11.5–30%) compared to studies on other belostomatids, which explains why subsequent binary prey choice experiments using one predator and two prey—either large and small females or male and female (with smaller sample sizes of n = 20 and 30, respectively)—did not confirm the results of our first experiment. Our study exemplifies how a pattern of body size-dependent predation can arise in a novel (not coevolved) predator–prey interaction. We tentatively argue that the observed pattern could be driven by intrinsic features of the predator, namely, altered prey preferences with increasing age coupled with a general preference for large-bodied prey, or changing nutritional needs at different developmental stages.
Forensic entomology
(2017)
For many members of the forensic community, insects still have an exotic status. This may be one reason why forensic entomology, the analysis of insect evidence for forensic and legal purposes, has not yet achieved the significance it deserves in forensic sciences. The present special issue may help to change that. ...
Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species
(2017)
The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.