Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be... Show moreEcological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free-living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole-nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size-adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera-recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68-0.94) at order level and at R = .75 (CI:0.67-0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds. Show less
Freshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species. European and national regulation... Show moreFreshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species. European and national regulation dictate the monitoring of freshwater quality in the Water Framework Directive. The biological elements of these assessments focus on the organisms living in freshwater systems, such as fish, macroinvertebrates, and plants. Traditional monitoring of quality relies on labor-intensive and expensive collection and morphological identification of specimens. Recent developments in molecular techniques allow for easier identification through (meta)barcoding and species detection using environmental DNA (eDNA). This thesis explores the possibilities to integrate genetic tools into freshwater quality monitoring and impact assessments, by investigating the ability of DNA-based methods to approximate morphologically determined species occurrences and the influence of their abundance on quality ratios. Additionally, it examines the effects of replication strategies in eDNA sampling, and studies the implications of using eDNA monitoring across several trophic levels of the ecosystem in impact assessments. Combined with a growing body of literature, the findings in this thesis illustrate that molecular techniques will contribute to a better ecosystem understanding and allow for more effective monitoring and management of freshwater systems, safeguarding the ecosystem services provided to humankind. Show less
DNA barcoding of Dutch collections of Ptychostomum rubens (Mitt.) Holyoak & N.Pedersen as understood in modern Floras revealed two distinct taxa. A morphological study of these specimens... Show moreDNA barcoding of Dutch collections of Ptychostomum rubens (Mitt.) Holyoak & N.Pedersen as understood in modern Floras revealed two distinct taxa. A morphological study of these specimens recognized several characters which can be used for identification. Ptychostomum rubens as well as its synonym Bryum bomanssonii Lindb. are lectotypified here. These lectotypes, and hence these two taxa, belong to the same morpho-molecular species. The other species is described here as a new species: Ptychostomum touwii Bijlsma, Kruijer & M.Stech. A key to these two species and the closely related P. bornholmense (Wink. & R.Ruthe) Holyoak & N.Pedersen is given. Their distribution and ecology in the Netherlands are briefly discussed. Ptychostomum rubens is a widespread species in the Netherlands, occurring on disturbed, base-rich, often calcareous and nutrient-rich soils, whereas P. touwii is calcifuge and prefers disturbed, less nutrient-rich, sandy soils and loams. The distribution range of the latter species needs to be clarified yet. After studying material from the South American species Bryum subapiculatum Hampe, B. dentiferum Hampe, and B. rubrinerve Cardot & Broth., we propose to exclude these species from the species concept of B. microerythrocarpum Müll.Hal. & Kindb. awaiting further molecular research of this variable species complex. Since, based on previous molecular research, B. subapiculatum is recently classified in the genus Imbribryum N. Pedersen and B. subapiculatum and B. microerythrocarpum are closely related, we also make the new combination Imbribryum microerythrocarpum (Müll.Hal. & Kindb.) Bijlsma, Kruijer & M. Stech. Show less
Welker, F.; Duijm, E.; Gaag, K.J. van der; Geel, B. van; Knijff, P. de; Leeuwen, J. van; ... ; Gravendeel, B. 2014
