Morphological and genetic variation in Hanleya nagelfar and Hanleya hanleyi (Mollusca: Polyplacophora) in the Northern European Atlantic and the phylogenetic position of Hanleyidae based on nuclear and mitochondrial genes

Large specimens of the spongivore Hanleya nagelfar (Mollusca: Polyplacophora) differ noticeably from the smaller congeneric H. hanleyi, but many scientists have reported that small specimens are very similar and perhaps identical. The debate of their relationship has been ongoing for over 140 years, without reaching a conclusion. This thesis uses genetics combined with statistical analyses on morphometric characters previously used for separating the two species, as well as examination of girdle armature and radulae, in the attempt to resolve the relationship of the chitons. Partial sequences of the genes 18S rRNA, 16S rRNA and cytochrome B are used to find differences within Hanleya. A Bayesian analysis is used to infer the molecular phylogenetic position of Hanleyidae among Polyplacophora for the first time. Statistical analyses find substantial ontogenetic changes in all external diagnostic characters. Radula and cytochrome b variations indicate presence of a hidden species within Hanleya in the Northern European Atlantic.Master i Marin biodiversitetMAMN-MARBIMARINDI

Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding

Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found that the diets of both collared (Dicrostonyx groenlandicus) and brown lemmings (Lemmus trimucronatus) on Bylot Island were dominated by Salix while mosses, which were significantly consumed only by the brown lemming, were a relatively minor food item. The most abundant plant taxon, Cassiope tetragona, which alone composes more than 50% of the available plant biomass, was not detected in feces and can thus be considered to be non-food. Most plant taxa that were identified as food items were consumed in proportion to their availability and none were clearly selected for. The resulting high diet overlap, together with a lack of habitat segregation, indicates a high potential for resource competition between the two lemming species. However, Salix is abundant in the winter habitats of lemmings on Bylot Island and the nonSalix portion of the diets differed between the two species. Also, lemming grazing impact on vegetation during winter in the study area is negligible. Hence, it seems likely that the high potential for resource competition predicted between these two species did not translate into actual competition. This illustrates that even in environments with low primary productivity food resources do not necessarily generate strong competition among herbivores

Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability

Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women’s healthcare for the treatment of endometriosis, known as Gui Zhi Fu Ling Wan (FL) and Ge Xia Zhu Yu Tang (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has a resolution for all species indirectly through the identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification, some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons are assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for the comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use

Morphological and genetic variation in Hanleya nagelfar and Hanleya hanleyi (Mollusca: Polyplacophora) in the Northern European Atlantic and the phylogenetic position of Hanleyidae based on nuclear and mitochondrial genes

Large specimens of the spongivore Hanleya nagelfar (Mollusca: Polyplacophora) differ noticeably from the smaller congeneric H. hanleyi, but many scientists have reported that small specimens are very similar and perhaps identical. The debate of their relationship has been ongoing for over 140 years, without reaching a conclusion. This thesis uses genetics combined with statistical analyses on morphometric characters previously used for separating the two species, as well as examination of girdle armature and radulae, in the attempt to resolve the relationship of the chitons. Partial sequences of the genes 18S rRNA, 16S rRNA and cytochrome B are used to find differences within Hanleya. A Bayesian analysis is used to infer the molecular phylogenetic position of Hanleyidae among Polyplacophora for the first time. Statistical analyses find substantial ontogenetic changes in all external diagnostic characters. Radula and cytochrome b variations indicate presence of a hidden species within Hanleya in the Northern European Atlantic

DNA Sequencing Historical Lichen Specimens

Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it

Testing hypotheses of hybrid origins for two seashore species of Carex section Phacocystis (Cyperaceae)

Abstract Taxonomists have proposed numerous hybrid species in plants, but to gain a better understanding of the role that hybridization may play in plant diversification, such taxonomic hypotheses must be tested using genomic data. In this study, we employ ddRAD sequence data to test taxonomic hypotheses of hybrid origins in Carex salina and C. ramenskii (Carex section Phacocystis). Sequence data from multiple Norwegian and Icelandic populations of the putative hybrid and parental species were generated for hundreds of ddRAD loci. These data were used to estimate geographical structuring of genetic diversity and admixture and to explicitly test for hybrid origins using several analytical approaches. Our results indicate recurrent hybrid origins for the populations of C. salina and C. ramenskii sampled in our study and show that these populations are characterized by high interspecific heterozygosity. Our results support the idea that hybridization may indeed play an important role in the diversification of lineages of Carex and highlight the important role that clonal propagation might play in maintaining hybrid populations. Future studies focusing on a broader geographical sampling would be needed to assess if the genetic structuring in these Nordic populations reflects range-wide patterns in these hybrid lineages

DNA Metabarcoding for Quality Control of Basil, Oregano, and Paprika

Herbs and spices are some of the most vulnerable products in terms of fraud and adulteration in the food sector. Although standard analytical methods are accurate for quality control of specific lead or marker compounds, they cannot accurately assess the entire species composition of many marketed products. Complementary analytical approaches are thus often used for comprehensive screening of herbs and spices. In this study we evaluate DNA metabarcoding for the identification and authentication of 62 products, containing basil, oregano, and paprika collected from different retailers and importers in Norway. Our results show varying degrees of discrepancy between the constituent species and those listed on the product labels, despite high product authenticity. We suggest the false positives result from the sensitivity of DNA metabarcoding and filtering thresholds should be integrated into protocols to reduce false positives. Our results highlight how integrating DNA metabarcoding into the toolbox of analytical methods for quality control of fresh and/or processed plant-based food can improve product quality

DNA Metabarcoding Reveals Diet Overlap between the Endangered Walia Ibex and Domestic Goats -Implications for Conservation

Human population expansion and associated degradation of the habitat of many wildlife species cause loss of biodiversity and species extinctions. The small Simen Mountains National Park in Ethiopia is one of the last strongholds for the preservation of a number of afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra walie. The narrow distribution range of this species as well as potential competition for resources with livestock, especially with domestic goat, Capra hircus, may compromise its future survival. Based on a curated afro-alpine taxonomic reference library constructed for plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of both species were collected from different localities in the National Park. We show that both species are browsers, with forbs, shrubs and trees comprising the largest proportion of their diet, supplemented by grasses. There was a considerable overlap in dietary preferences. Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic goat. These results indicate that there is potential for competition between the two species, especially during the dry season, when resources are limited. Our findings, in combination with the expected increase in domestic herbivores, suggest that management plans should consider the potential threat posed by domestic goats to ensure future survival of the endangered Walia ibex

Holistic multi-method survey to enhance Madagascar's freshwater fish conservation

<p>Freshwater ecosystems are crucial for global biodiversity, supporting plant and animal species and providing essential resources. However, these ecosystems, particularly in island environments such as Madagascar, are under significant threat. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species <i>Rheocles derhami</i>, last recorded in 2013. To assess the status of this and other threatened fish species including <i>Ptychochromis insolitus</i> and <i>Paretroplus gymnopreopercularis</i>, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. Our findings reveal updated records of <i>Rheocles derhami</i> and an expanded species list within these freshwater environments. We also explore the implications of combining these two monitoring approaches and investigate the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primers targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provide 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study enlightens the current state of freshwater biodiversity in Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.</p&gt

Genomic evidence of speciation reversal in ravens

Speciation reversal is known mainly from recently diverged lineages that have come into secondary contact following anthropogenic disturbance. Here, Kearns et al. use genomic and phylogenomic analyses to show that the Common Raven (Corvus corax) was formed by the ancient fusion of two non-sister lineages of ravens