Biology subjects

Yoccoz, N.

Publications and source records attributed to Yoccoz, N..

3 recordsLinked to original sources

bioRxiv2025

Capture probe, metabarcoding, or shotgun sequencing: which best reflects local vegetation?

O_LIMetabarcoding is the most widely applied method for studying plant communities using environmental DNA, with shotgun sequencing and capture probes being alternative methods. Any methods ability to detect and correctly identify plant taxa may vary with DNA preservation, DNA reference library and the size of the local flora, making it difficult to compare results from different environments. C_LIO_LIHere we compare these methods using lake surface-sediments from Northern Fennoscandia with the PhyloNorway genome skim reference library (1500 taxa) that includes almost all species of the regional flora. We also undertook vegetation surveys from around the lakes to estimate the true positive detection rate, identify false positive detections, and provide optimal filtering cut-off thresholds for the three methods. C_LIO_LIOptimal filter cutoffs were one PCR replicate and 3 reads for metabarcoding, and 3.2x10e-6 and 5.6x10e-6 of queried reads, respectively, for the shotgun and capture probe data. Applying these thresholds, the rate of false positives was too high for reliable identification at species level based on shotgun (49%) and capture probes (62%), whereas it was low for metabarcoding (5-12%). All methods were reliable at genus and family levels after applying the optimal filtering thresholds (<4% false positives). Our results show that metabarcoding on average detects 2.1 times as many true positive taxa as shotgun sequencing, and 6.4 times as many taxa as capture probes. Proportions of filtered metabarcoding and shotgun reads were significantly related to abundance categories from vegetation surveys, but this was not the case for capture probe data. C_LIO_LIWe expect the false positive rate of shotgun sequencing to decrease with increasing genome completeness in the reference libraries, and be advantageous for highly degraded DNA with fragments too short for metabarcoding. At present, metabarcoding provides the highest detectability and taxonomic resolution for correct identification of vascular plants. C_LI

ecology↗

bioRxiv2022

Arctic evergreening - encroaching allelopathy in a management blind spot

O_LIOngoing Arctic greening can increase productivity and reindeer pasture quality in the tundra. However, greening may also entail proliferation of unpalatable species, with distinct consequences for pastoral socio-ecological systems (SES). C_LIO_LIWe show extensive greening across 20 reindeer districts in northern Norway between 2003 and 2020. The allelopathic, evergreen dwarf-shrub crowberry biomass increased by 60%, contrasted by smaller increases of deciduous dwarf-shrubs and stagnating forb and graminoid biomass. C_LIO_LIWe found evidence, although uncertain, of a negative relationship between biomass and reindeer densities, but only among forbs, the least abundant plant group. C_LIO_LIOur results challenge the management decision-making, which aims at sustainable pasture management, but which assumes stationary density-dependent relationships. Changes in temporal vs. spatial relationships should be included as management criteria, to avoid mismanaging a SES in transition. C_LIO_LILarge-scale shift towards increased allelopathy may undermine the resource base of a key Arctic herbivore and pastoral SES. C_LI

ecology↗

bioRxiv2019

Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)

O_LIIn species providing extended parental care, one or both parents care for altricial young over a period including more than one breeding season. We expect large parental investment and long-term dependency within family units to cause high variability in life trajectories among individuals with complex consequences at the population level. So far, models for estimating demographic parameters in free-ranging animal populations mostly ignore extended parental care, thereby limiting our understanding of its consequences on parents and offspring life histories. C_LIO_LIWe designed a capture-recapture multi-event model for studying the demography of species providing extended parental care. It handles statistical multiple-year dependency among individual demographic parameters grouped within family units, variable litter size, and uncertainty on the timing at offspring independence. It allows to evaluate trade-offs among demographic parameters, the influence of past reproductive history on the caring parent survival status, breeding probability and litter size probability, while accounting for imperfect detection of family units. We assess the model performances using simulated data, and illustrate its use with a long-term dataset collected on the Svalbard polar bears (Ursus maritimus). C_LIO_LIOur model performed well in terms of bias and mean square error and in estimating demographic parameters in all simulated scenarios, both when offspring departure probability from the family unit occurred at a constant rate or varied during the field season depending on the date of capture. For the polar bear case study, we provide estimates of adult and dependent offspring survival rates, breeding probability and litter size probability. Results showed that the outcome of the previous reproduction influenced breeding probability. C_LIO_LIOverall, our results show the importance of accounting for i) the multiple-year statistical dependency within family units, ii) uncertainty on the timing at offspring independence, and iii) past reproductive history of the caring parent. If ignored, estimates obtained for breeding probability, litter size, and survival can be biased. This is of interest in terms of conservation because species providing extended parental care are often long-living mammals vulnerable or threatened with extinction. C_LI

ecology↗