Species identification
EcoGene have an extensive range of tests available to identify a species from various different types of samples.
DNA retrieved from a sample of unknown material is compared to reference or already identified DNA sequences using either an online international DNA reference database or our in-house EcoGene database. Where possible, we only use sequences for comparison that have originated from a formally identified specimen.
Examples where species identification testing can help:
- Predatory animal species detection. Samples acquired include wound sites, eggshells, hair snags and scat
- Identify the presence of a predatory or invasive pest species. This enables their detection in an area thought to be free from predators. Samples are acquired from hair and faeces
- DNA testing to identify different plant species
- Gut content analysis for identification of food items using DNA-based tests for prey species of interest
- Wildlife forensics for items seized at the border, such as traditional medicines or ivory figurines for breaches of CITES regulations
- Identification of invertebrate species. Samples acquired include eggs, larvae and fragments using DNA-based methods
Genotyping and Monitoring
We offer genotyping services for a variety of applications:
Genotyping to support conservation
EcoGene can help determine conservation management units, support translocation programmes, and provide data and advice for captive breeding programmes. Similarly, appropriate markers can be adapted and implemented for species where published information is available.
We have expertise and genetic markers for a wide range of species that include stoat, ferret, dog, cat, mouse, rabbit, rat, ungulates (deer, goat, and pig), possum, invertebrates (giant wētā, Powelliphanta snail), reptiles (geckos and skinks), and native bird species (tūī, pīwakawaka/fantail, kiwi, ōi/grey-faced petrel, pāteke/brown teal and whio/blue duck).
Population monitoring, particularly introduced mammalian pests:
Management of wild animal populations usually requires some assessment of abundance. EcoGene have developed methods involving a simple tube design for sampling hair from a range of key vertebrate pests. ‘Passive’ (non-invasive) methods are often better for cryptic or trap-shy species, especially when they are at low population density in the landscape.
Detecting species
DNA data can help determine the presence of a species - either a new invasion or re-immigration following pest control. This can help identify sources of immigrants (where appropriate population databases are available) as well as likely frequency for control operations.
Species can be identified from the presence of samples such as hair or scat. A second test can then be used to match back to an individual. This is important when an incursion has recently been detected in a pest-free area as it can identify whether such samples were derived from one or more individuals. This testing beyond species identification is reliant on the recovery of DNA that is of sufficient quality and quantity, it may not be possible for poor quality or old samples.
Individual identification and population of origin
Where sufficient population data exist, individual identification can be used to assign individuals to a population of origin. It is also used to identify a particular individual of a species, e.g. samples taken from wounds of a predated kiwi have the potential to identify the likelihood of DNA being from a particular dog. For an incursion response or an eradication programme this can be useful where a match is required between samples and a specimen, e.g. to confirm the capture of an individual.
Sex and parentage analysis
We have a range of markers available for sex identification in mammals, birds, some reptiles and amphibians. We can also carry out paternity analysis if an appropriate number of samples are provided and/or if a larger database exists.
Microbe and Fungi DNA diagnostics
Microbial culture
Species identification from pure bacterial, fungal, and chromist cultures
Our standard approach consists of DNA extraction, sequence of a single gene (Fungal ITS or bacterial 16S) in both directions and best match identification with reference databases. Custom and complex identifications are also available.
Additional services
- Storage of cultures in the International Collection of Microorganisms from Plants (ICMP) culture collection. Entries to the collection are usually publicly available, but we do offer a private use only option.
- Storage of dried fungal and plant disease specimens in the New Zealand Fungarium (PDD) collection.
- Metagenomic profiling
For more information on EcoGene Microbial services please contact our Microbial Science Advisor: Bevan Weir.
Disease screening
EcoGene tests for:
- Avian malaria – this vector-borne disease is prevalent in New Zealand. We offer a screening service for avian malaria using PCR from bird blood samples.
- Whataroa virus - Whataroa virus is an arthropod-borne group A arbovirus isolated in South Westland, New Zealand, in 1962. We can screen bird blood samples for this virus using reverse transcriptase PCR.
- Murine typhus - this flea-borne rickettsial rodent disease can spill over to humans causing a non-specific illness. We provide screening of rat blood samples to detect for the presence of this disease.
- Chytrid fungus – this infectious fungus is devastating amphibian populations globally. We can provide the standardised service for chytrid fungus detection from both swab and tissue samples derived from infected individuals.