Ecogenics GmbH

Zurich, Sweden

Ecogenics GmbH

Zurich, Sweden
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Ramstad K.M.,Victoria University of Wellington | Pfunder M.,Ecogenics GmbH | Robertson H.A.,Research and Development Group | Colbourne R.M.,Research and Development Group | And 3 more authors.
Conservation Genetics Resources | Year: 2010

We present 14 microsatellite loci that were isolated from little spotted kiwi (LSK, Apteryx owenii). All loci cross-amplify in all kiwi species currently recognized except for one locus in a single species. Little spotted kiwi exhibited lower variation at these loci (mean number of alleles, H E) than other kiwi species, despite the markers having been developed for polymorphism in LSK and a far greater number of LSK genotyped than kiwi of other species. Reliable cross-species amplification and polymorphism make these markers promising new tools for the management of New Zealand's threatened kiwi. © Springer Science+Business Media B.V. 2010.

PubMed | Ecogenics GmbH
Type: Journal Article | Journal: Environmental toxicology and chemistry | Year: 2016

In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications. Environ Toxicol Chem 2016;35:1970-1977. 2015 SETAC.

Ismail S.A.,ETH Zurich | Buser A.,Ecogenics GmbH | Uma Shaanker R.,University of Agricultural Sciences, Bangalore | Ravikanth G.,Ashoka Trust for Research in Ecology and the Environment | And 2 more authors.
Conservation Genetics Resources | Year: 2013

Vateria indica (Dipterocarpaceae) is an economically and ecologically important canopy tree endemic to the Western Ghats, India. The species has undergone extensive habitat loss and overexploitation and is therefore listed as 'critically endangered' on the 2012 IUCN Red List. We developed ten polymorphic microsatellite loci for V. indica. In addition, we confirm cross amplification and variation in two loci isolated from the closely related but geographically disjunct species Vateriopsis seychellarum, previously published by Finger et al. Conserv Genet Resour, 2 (S1):309-311, (2010). The twelve microsatellite primers screened on 48 adult samples of V. indica had 5-11 alleles per locus (mean of 8. 5 per locus) with an average polymorphic information content of 0. 64 across loci. Expected heterozygosity ranged from 0. 44 to 0. 84. These markers will enable us to quantify population genetic diversity in habitat fragments and to study fine scale spatial genetic structure and contemporary gene flow. © 2012 Springer Science+Business Media Dordrecht.

PubMed | Ecogenics GmbH, ETH Zurich, TU Darmstadt and Seychelles Islands Foundation
Type: Journal Article | Journal: Applications in plant sciences | Year: 2016

The evolutionarily and ecologically distinct coco de mer palm Lodoicea maldivica (Arecaceae) is endemic to two islands in the Seychelles. Before colonization of the islands by man, the endangered palm formed large monodominant stands, but its natural range is now restricted to four main populations and several patches of isolated individuals. Microsatellite markers were designed to investigate the genetic structure of the remaining natural populations of L. maldivica.We developed 12 polymorphic and three monomorphic microsatellite markers for this species, with a mean number of alleles per locus of 13.2 (range 5-21) and expected heterozygosity values ranging from 0.31-0.91 for the polymorphic loci.These markers enable us to study the patterns of genetic diversity, contemporary seed dispersal, and the fine-scale spatial genetic structure of this important conservation flagship species.

Audzijonyte A.,Nature Research Center | Audzijonyte A.,University of Helsinki | Haugstetter J.,Ecogenics GmbH | Arbaciauskas K.,Nature Research Center
Conservation Genetics Resources | Year: 2014

Paramysis lacustris is a Ponto-Caspian mysid crustacean species. It inhabits coasts, estuaries and lower parts of rivers in the Black, Azov and Caspian seas and shows high levels of genetic structuring and cryptic diversity. The species has been introduced into the Baltic Sea basin and is considered to be a high risk invader. We developed ten microsatellite loci and tested their polymorphism in 70 individuals from four wild populations. The number of alleles per locus ranged from 4 to 23; none of the loci showed consistent deviations from Hardy-Weinberg equilibrium. These microsatellite markers will be useful to trace potential invasions and understand dynamics of native P. lacustris populations. © 2013 Springer Science+Business Media Dordrecht.

Gamero A.,University of Gottingen | Gamero A.,Behavioural Ecology and Sociobiology Unit | Buser A.,Ecogenics GmbH | Kappeler P.M.,University of Gottingen | Kappeler P.M.,Behavioural Ecology and Sociobiology Unit
Conservation Genetics Resources | Year: 2013

We characterized 10 specific microsatellite loci for White-breasted mesites (Mesitornis variegata), an endemic bird species from western Madagascar. Nine loci were in Hardy-Weinberg equilibrium, and we detected 4-10 alleles per locus (mean = 6. 1). These primers will be used to study the mating system and social organization of White-breasted mesites and may have applications for the conservation of the few remaining populations of this vulnerable and still poorly studied species. © 2013 The Author(s).

Schultz J.K.,Hawaii Institute of Marine Biology | Marshall A.J.,University of Otago | Pfunder M.,Ecogenics GmbH
Diversity | Year: 2010

Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the genome. Heterozygosity is lost more slowly and is severely impacted only when populations are small for an extended period of time. We test the hypotheses of selective sweep, historical bottleneck and persistently small population size to explain extremely low genetic diversity in the critically endangered Hawaiian monk seal (Monachus schauinslandi). Of 163 microsatellite loci isolated from the species' genome, only 17 are polymorphic. Mapping 98 monomorphic and 12 polymorphic loci to 35 chromosomes throughout the dog genome, we reject the selective sweep hypothesis. Genotyping 2,423 Hawaiian monk seals at the 17 polymorphic loci plus a locus previously isolated from another pinniped species, we find evidence for a recent bottleneck (P = 0.04). This is consistent with historical records describing intense hunting in the 19th century; however, the bottleneck was not of sufficient severity and duration to explain the genome-wide depletion of genetic diversity (H O = 0.05; A = 1.1). Long-term population size restriction is a more likely explanation. Though at least two of the polymorphic loci appear to be candidates for selection, the low genetic diversity of the species may further threaten chances for survival of this critically endangered species in a changing world. © 2010 by the authors; licensee MDPI, Basel, Switzerland.

Angles d'Auriac M.B.,Norwegian Institute for Water Research | Hobaek A.,Norwegian Institute for Water Research | Christie H.,Norwegian Institute for Water Research | Gundersen H.,Norwegian Institute for Water Research | And 3 more authors.
BMC Research Notes | Year: 2015

Background: The green sea urchin Strongylocentrotus droebachiensis has a wide circumpolar distribution and plays a key role in coastal ecosystems worldwide by destructively grazing macroalgae beds and turn them into marine deserts, so-called barren grounds. In the past decades, large established kelp forests have been overgrazed and transformed to such barren grounds on the Norwegian coast. This has important repercussions for the coastal diversity and production, including reproduction of several fish species relying on the kelp forests as nurseries. Genetic diversity is an important parameter for the study and further anticipation of this large scale phenomenon. Findings: Microsatellites were developed using a Norwegian S. droebachiensis individual primarily for the study of Northeast Atlantic populations. The 10 new microsatellite loci were amplified using M13 forward tails, enabling the use of M13 fluorescent tagged primers for multiplex reading. Among these loci, 2 acted polysomic and should therefore not be considered useful for population genetic analysis. We screened 96 individuals sampled from 4 different sites along the Norwegian coast which have shown unexpected diversity. Conclusions: The new microsatellite loci should be a useful resource for further research into connectivity among S. droebachiensis populations, and assessing the risks for spreading and new overgrazing events. © 2014 Anglès d'Auriac et al.; licensee BioMed Central Ltd.

Kery M.,Swiss Ornithological Institute | Gardner B.,U.S. Geological Survey | Stoeckle T.,University of Basel | Stoeckle T.,Ecogenics GmbH | And 2 more authors.
Conservation Biology | Year: 2011

Assessment of abundance, survival, recruitment rates, and density (i.e., population assessment) is especially challenging for elusive species most in need of protection (e.g., rare carnivores). Individual identification methods, such as DNA sampling, provide ways of studying such species efficiently and noninvasively. Additionally, statistical methods that correct for undetected animals and account for locations where animals are captured are available to efficiently estimate density and other demographic parameters. We collected hair samples of European wildcat (Felis silvestris) from cheek-rub lure sticks, extracted DNA from the samples, and identified each animals' genotype. To estimate the density of wildcats, we used Bayesian inference in a spatial capture-recapture model. We used WinBUGS to fit a model that accounted for differences in detection probability among individuals and seasons and between two lure arrays. We detected 21 individual wildcats (including possible hybrids) 47 times. Wildcat density was estimated at 0.29/km2 (SE 0.06), and 95% of the activity of wildcats was estimated to occur within 1.83 km from their home-range center. Lures located systematically were associated with a greater number of detections than lures placed in a cell on the basis of expert opinion. Detection probability of individual cats was greatest in late March. Our model is a generalized linear mixed model; hence, it can be easily extended, for instance, to incorporate trap- and individual-level covariates. We believe that the combined use of noninvasive sampling techniques and spatial capture-recapture models will improve population assessments, especially for rare and elusive animals. ©2010 Society for Conservation Biology.

Pompini M.,University of Lausanne | Buser A.M.,Ecogenics GmbH | Thali M.R.,Ecogenics GmbH | Von Siebenthal B.A.,University of Lausanne | And 4 more authors.
Journal of Fish Biology | Year: 2013

On the basis of the experiments carried out over various years, it was concluded that (1) grayling Thymallus thymallus and brown trout Salmo trutta are resistant to temperature-induced sex reversal at ecologically relevant temperatures, (2) environmental sex reversal is unlikely to cause the persistent sex ratio distortion observed in at least one of the study populations and (3) sex-specific tolerance of temperature-related stress may be the cause of distorted sex ratios in populations of T. thymallus or S. trutta. © 2013 The Fisheries Society of the British Isles.

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