News

Updates and insights from AMS research projects.



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Identifying moulds in homes

Humid air or condensation is one of the most significant contributors to dampness in homes. Moisture not only can damage the structure of homes, but it can also promote the growth of mould. Mould has been linked to various health issues such as allergies, asthma and sick building syndromes. Therefore, having drier houses also means healthier homes.

The most effective method to reduce dampness is by creating ventilation in homes. It includes opening windows and doors to get airflow between indoors and out. Alternatively, home ventilation systems (HVS) achieve similar movement by blowing dry air indoors from the roof spaces in houses. 

But how effective is an HVS in really removing dampness in houses? The AMSRC lab is leading a research study looking into the effect of an HVS on mould growth in homes. This research is part of a larger project investigating the impact of HVS on indoor air quality led by Associate Professor Teri-Ann Berry and her IAQ Research Team. Using a molecular genetics approach, we can identify the species composition and amount of mould growth in homes to detect changes in mould presence following the installation of HVS. All we need are samples of surface swabs, dust or air from houses.

How do we identify mould species? We use Next Generation Sequencing, which enables us to target specific regions of mould DNA and to sequence the DNA from multiple species all at once. We will then identify species using global genetic databases. Currently, there is not much knowledge on the diversity of mould species found in New Zealand homes. This study will obtain some baseline information on moulds and potentially identify important species that may be linked to human health issues or ones associated with water damage in buildings in New Zealand.

How do we quantify the amount of mould? We use real-time PCR (similar equipment to that being used to detect COVID-19), which can estimate the amount of mould DNA in the sampled environment. Quantity of DNA is usually used as a proxy for estimating the amount or number of organisms present – more DNA detected suggests more mould in the environment. Here, we will quantify specific moulds of potential health concern (e.g. AspergillusPenicilliumStachybotrys) and the overall mould DNA present in the sampled environment before and after installation of the HVS. If the HVS is able to suppress moulds’ growth and production, we would see overall mould DNA to be significantly less post-installation. A significant reduction in mould would suggest that the HVS may effectively prevent or reduce human health issues associated with damp housing.

In a pilot study last year, we collected swab and dust samples from different rooms in a single house before and after the installation of an HVS. We wanted to identify the types of mould found in the home and if species diversity changes after installing an HVS. Here, we first cultured the samples to isolate pure mould species before sequencing their DNA. We found that each room had different types of mould species, and it varied after the installation of an HVS. In particular, the number of species in the bathroom significantly dropped post-installation. We detected various airborne moulds and mould species brought into the house by the occupants (e.g. on shoes, bags, clothes). We found some moulds associated with humidity (e.g. Cladosporium spp.) and potentially pathogenic to humans (e.g. Penicillium spp., Rhodotorula spp.) and sheep (Pithomyces chartarum)! The  latter, we suspect, was either wind-blown or brought in by the occupants from outdoors.

This year, we will continue with the main study, which involves sampling from various homes from two cities in New Zealand. Our research will feedback to the larger multidisciplinary project (engineering: air quality and social sciences: lifestyle) to provide a more complete and meaningful picture on maintaining healthy homes in New Zealand.

Dr Marleen Baling

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What is it like studying at Unitec?

For more information check out the programme pages on the Unitec website

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AMS Summer Intern 2020/2021

Holly Goodman, a second year Unitec Bachelor of Applied Science student, was awarded an AMS summer studentship to work on a project on comparing the effectiveness of different sampling techniques for detecting Cryptosporidia in native reptiles. She will be supervised by Dr Marleen Baling. The project is a collaboration with Dr An Pas, senior vet at Auckland Zoo.

Holly is originally from Southampton, England, and she moved to New Zealand when she was 6 years old. She has always had a passion for animals and currently work part-time in a doggy day care facility. Holly started at Unitec studying for the NZ Certificate in Animal Care, which then led her to a Bachelor of Applied Science in 2019. Through the degree she found a profound love for reptiles and amphibians. Holly’s future aspirations are to learn more about New Zealand’s native herpetofauna and contribute to their conservation. Alongside her love of animals, she enjoys drawing, singing and playing football.

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Fifty shades of prey: extreme colour polymorphism in an endemic marine isopod

Fifty shades of prey: extreme colour polymorphism in an endemic marine isopod

Colour polymorphism is defined as colour variation within a species or population that is maintained by genes in our DNA (rather than by diet or the environment). Many animals exhibit some degree of colour polymorphism. This can simply be displayed as different shades of brown, or right through to completely different colours such as the red, green, yellow, blue and black colour morphs found in poison dart frogs.

However, few organisms show such extreme degrees of colour polymorphism as Isocladus armatus, a New Zealand endemic marine isopod. These little guys, which can be found swimming about in intertidal rock pools all along the NZ coastline, range in colour from purple, white, red, green, brown, sand, grey, orange, as well as showing distinct colour patterning such as a long white stripe down their back, variegated, or with a single white spot on their back. They seem to be so variable that they have been described as “no two individuals being alike”.

Fig. 1: Some of the colour morphs in I. armatus: (a) and (f) variegated, (b) and (g) striped, (c) green, (d) white, (e) grey, (h) spotted.

Fig. 2. Isocladus armatus habitat on the Kaikoura peninsula.

The question therefore is, why? These colour morphs can be found in every population from populations in Northland, right through to populations in the South Island. Anecdotal evidence also suggests that this colour polymorphism has persisted across multiple speciation events, with other closely-related species of Isocladus in NZ displaying the same or similar colour morphs. This indicates that colour polymorphism must have a function in increasing survival and that natural selection favours the existence of multiple different colour morphs. My research, in collaboration with scientists at Massey University and Northern Arizona University in the USA, aims to investigate what factors have led to the evolution of this colour polymorphism.

Fig. 3. Three putative camouflage strategies adopted by I. armatus. (a) background matching – prey avoid detection by matching the colour, lightness and pattern of the habitat substrate; (b) disruptive colouration – prey break up their true outline with patterns which create false edges and boundaries; (c) masquerade – prey resemble an uninteresting object such as a shell fragment.

It is thought that this colouration functions in camouflaging the isopods from predators such as seagulls and fish. Indeed, this camouflage works so well against the background of a sandy rock pool that it can often be virtually impossible to see them! The white stripe in particular works well as a disguise in which they can resemble a shell fragment. But why maintain all these different camouflage strategies? Why have these isopods not evolved to just all have the one most effective colour morph type? Our research tests multiple explanations for this.

Fig. 4. Isocladus armatus can often be found swimming around upside down in intertidal rock pools such as these.

One possibility is that colour polymorphism within populations is maintained by migration, or gene flow, between populations. This process effectively homogenises colour variation so that each colour morph occurs at the same frequency in every population. We are testing this hypothesis by investigating levels of gene flow across different spatial scales across NZ. Published as a series of two papers in PeerJ (Wells & Dale 2018) and Ecology and Evolution (Pearman et al. 2020), we used a next-generation-sequencing technique called genotyping-by-sequencing to unlock and investigate genetic variation at 8,000 single nucleotide polymorphisms (SNPs) across the genome. This allows us to investigate connectivity between populations at a very high resolution. We found that dispersal in this species mostly follows an Isolation-By-Distance model, in which gene flow occurs mostly between neighbouring populations, with genetic differences between populations increasing with the distance between populations. This type of dispersal could be responsible for maintaining the colour polymorphism within each population, even if different specific morphs provide the best camouflage in different populations.

Fig. 5. Procrustes transformation of a PCA based on 8,000 SNPs overlaid onto geographical space. Dots are I. armatus individuals coloured by population. Arrows indicate actual geographical location of the genetic clusters, revealing that genomic variation is mostly concordant with geography.

Because this colour polymorphism also seems to occur in other Isocladus species, we are also using DNA to build phylogenies of all the Isocladus species in NZ. We will then use this to investigate how colour polymorphism has been maintained through multiple speciation events. There are so far 6 known species of Isocladus throughout NZ and the Chatham Islands, however our preliminary research suggests that there may be cryptic species present.   

Some colour morphs are more common in warmer or colder waters of NZ. This, combined with their abundance throughout the NZ coastline, means that this species has the potential to be a bio-indicator of climate change and the increase in sea surface temperatures. Future research will sequence the entire genome to investigate what genes may be responsible for colouration and what function they have in relation to fitness in different temperature environments.

Contact
Dr Sarah Wells
svanwinkel@unitec.ac.nz

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A new staff member for AMS

A new staff member has recently joined the Applied Molecular Solutions Research Centre team. Tianyi Tang gained his Masters degree in Biological Sciences at the University of Auckland and Plant and Food Research. In his thesis project, he investigated the possibility of using fungal endophytes to protect New Zealand grapevines against Grapevine Trunk Diseases (GTD), which are caused by multiple fungal pathogens.

At the Applied Molecular Solution Centre here at Unitec, he is working on different applications of fungi in a variety of projects. Some fungal species may be promising for the biological control of the invasive weed climbing asparagus (Asparagus scandens), others are being investigated to see if they may be able to reduce the toxicity of asbestos waste.

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Phylogeography of whau (Entelea arborescens) - Peter de Lange

Phylogeography of whau (Entelea arborescens) – Peter de Lange

As a result of molecular systematics Aotearoa / New Zealand now has very few endemic plant genera left. One of the few remaining endemic genera is Entelea of which whau (E. arborescens) is the sole known species. Whau is easily recognised by the large, soft, vaguely ‘heart-shaped’ leaves; by the clusters of attractive white flowers and spherical spinose fruits (de Lange 2019). Whau is also famous for its light wood reputed be to even lighter and more buoyant than balsa wood (Ochroma pyramidale). The pale-brown wood it produces is also unusual in that it is laid down in bands of unlignified pith-like parenchyma, such that no ‘growth rings’ are formed. Whau was originally placed in the Tiliaceae but molecular systematics and subsequent chemical and morphological research has merged that family with the Malvaceae. Interestingly whau is most closely related to the Afro-Madagascan genus Sparrmannia (Brunken & Muellner 2012; Benor 2018); notably both species have similar growth habits, wood, leaf shape and texture, flowers and fruits (Figure 1.).

Figure 1. Sparrmannia ricinocarpa. Image: Robert van Bittersdorf.

Whau is a common tree around the Auckland Region an abundance appreciated by Māori as can be seen by the names Maungawhau (Mt Eden) and Te Whau (Whau River). The species is indigenous to the Three Kings, North and South Islands, but within that range it is most common in the northern North Island in coastal sites. As a palatable species it is now most frequently seen where introduced browsing animals are uncommon or absent such as on the offshore islands within the Hauraki Gulf and Bay of Plenty, or in places where these animals are controlled. Thankfully whau, as a fast growing and attractive flowering small tree is also widely cultivated, and in Auckland it is a feature of many roadside plantings, especially as part of the ‘roadside restoration vegetation amalgam’ cynically known in the ecological consultancy trade as ‘Transit Scrub’. For an excellent example of this vegetation association look either side of ‘Spaghetti Junction’ next time you traverse inner Auckland.

Modern plantings aside though the apparently natural distribution of whau has intrigued people because the species is (or was) most common from about northern Taranaki and Mahia Peninsula north but south of here it occurs in scattered sites along the Eastern Wairarapa coast, at Cape Palliser, near Paekakariki and around Wellington. The species is also locally common in the coastal scrub and forest of the Golden Bay region of North West Nelson. Whilst some of these southerly North Island locations are undoubtedly the result of recent post European settlement deliberate plantings, Kapiti Island for example, others of longer standing presence are more problematic. Although the disjunction of Entelea to Golden Bay has parallels with the disjunction of kawaka (Libocedrus plumosa), tanekaha (Phyllocladus trichomanoides) the sedge Lepidosperma neozelandicum (Allan 1961; Moore & Edgar 1970) amongst others; the ‘spot’ occurrences in the southern North Island are less easily explained as part of some natural floral disjunction. Consequently, these occurrences along with those noted in the central Waikato and around the Rotorua lakes, have been the source of speculation and debate amongst botanists some of whom have suggested that they stem from deliberate plantings by Māori (Leach & Stowe 2005). Māori are known to have used whau wood, for example Ngati Porou used the wood for floats on nets (Best 1925), while the leaves were used for nappies and sanitary items; the foliage and flowers (Figure 2.) of whau was also used in ceremonies, notably at tangi (Riley 1994). However, these reported usages came from iwi who live within the accepted natural range of the species. Reports of the domestication of whau is therefore speculative and it was for this reason that a DNA based study of whau was initiated in 2009 to see whether whau was domesticated, or at least planted, over some parts of its range by Māori (Shepherd et al. 2019).

Figure 2. Whau flowering material. Image: Peter de Lange.

That study has now been completed and the results published in the New Zealand Journal of Botany (Shepherd et al. 2019). For the research 73 samples spanning the range of whau were analysed using two chloroplast loci (trnS(UGA)trnfM(CAU) and psbD-trnT(GGU)), the nuclear ITS region and also genotyped nine microsatellite loci.

The study found an unusual pattern; there is an East – West split in the northern range of whau which has hitherto not been noted in other phylogeographic studies of New Zealand coastal plants. The study also found that in the southern part of the species range, in sites where it was suggested whau had been planted that there was a mix of these lineages.

The East – West split within Entelea is estimated to have happened during the Pleistocene. Why this split occurs is problematic, it makes little sense in relation to the current understanding of New Zealand geological or environmental events. While there are as yet no known plant examples duplicating this pattern, the same pattern is evident in far north populations of shore skink (Oligosoma smithii) – though that split is dated to the Pliocene (Hare et al. 2008), and is also seen in kauri snail (Paryphanta busbyi) (a split dated as late Pliocene early Pleistocene) (Spencer et al. 2006). Again, for these animals no sensible explanation has been offered for the splits or the timing of them.

The study found two places where there was a mixing of lineages, the Auckland Region and in the southern range of whau. In the Auckland Region this pattern may be natural. The separation between East and West Coasts here is after all the narrowest in the country. However, it may also reflect that whau has been widely planted in this area over the last forty or so years by local councils, restoration groups and private individuals in Auckland using a range of often unspecified local sources.

The mixing of both lineages in the southern populations of whau is less easily explained. Here the mixing, coupled with the lack of novel genetic variation (chloroplast haplotypes, ITS alleles and microsatellite alleles), does infer that these occurrences could be the result of translocation by Māori. Certainly, it indicates that these populations have not been isolated for sufficient time for novel variation to have evolved, and that they stem from multiple origins. However, the wide distributions of each lineage within northern North Island prevents the identification of the precise sources of these southern populations, which contrasts with studies of other plants now known to have been domesticated and moved by Māori e.g., titirangi (Hebe (Veronica) speciosa) and rengarenga (Arthropodium cirratum) (Armstrong & de Lange 2005; Shepherd et al. 2016; Shepherd et al. 2018). These species have high levels of structuring in their natural populations allowing the origins of the cultivated populations to be determined.  Furthermore, the putative translocated populations of rengarenga and titirangi were genetically more similar to more distant populations than the geographically-closest natural populations, supporting their origin through human-mediated dispersal. For whau, the wide distribution of the genetic clusters in the northern part of that species range prevents determination of the source of these southern populations such that at least for now, a natural origin via long dispersal from the northern range of whau cannot be excluded.

Figure 3. Whau spinose fruits. Image: Peter de Lange.

These findings provide rich fodder for future studies of this singular plant. How, for example, is whau dispersed? Past wisdom has assumed that because whau has spinose fruits (Figure 3.) then these must have been dispersed by animals, otherwise why have the spines? Most recently Thorsen et al. (2009) speculated that whau fruits would have been moved by animals, which one assumes in pristine Aotearoa / New Zealand were probably species of moa, yet there is no evidence this happened, and indeed I have not yet seen any of our contemporary large feral animals such as horses, cattle or goats moving whau fruits around. The current genetic evidence doesn’t support animal movement either after all if our extinct moa did move whau, then surely one would expect there to be a mix of genetic lineages rather than the current genetic split because moa were widespread within the northern range of whau, and these birds almost certainly traversed the narrow Northland Peninsula and Te Aupouri isthmus. What I have seen is the fruit cases floating on water, and cast up along beaches and stream sides, and others have reported the fruits as wind-dispersed, noting that in strong breezes the fruits are rolled along beaches, dunes and bare hill slopes. Nevertheless, the way the fruit cases dehisce from top to bottom, and the ‘pepper pot’ way in which the seeds are dispersed well before the fruit cases drop does not support wind or water dispersal either. So, ruling out animal, water or wind dispersal, it would seem that something has contained whau for sufficient time to allow the split to develop. Maybe it is ecological; whau doesn’t thrive in dense forest, it needs regular disturbance and is cold sensitive, so perhaps the interior vegetation of Northland was too dense and conditions too cold to allow it grow there? Currently we don’t know. What we do know is that we have an intriguing pattern that deserves further study. Also, we are left without any clear resolution of whether the current distribution of whau is natural or in part stems from past planting by iwi.

References

Allan, H.H. 1961: Flora of New Zealand. Vol. I. Government Printer, Wellington

Armstrong, T.T.J.; de Lange, P.J. 2005: Conservation genetics of Hebe speciosa (Plantaginaceae) an endangered New Zealand shrub. Botanical Journal of the Linnean Society 149: 229–239.

Benor, S. 2018: Molecular phylogeny of the genus Corchorus (Grewioideae, Malvaceae s.l.) based on nuclear rDNA ITS sequences. The Crop Journal. 6: 552–563.

Best, E. 1925: The Maori Canoe. An account of various types of vessel used by the Maori of New Zealand in former times, with some description of these isles of the Pacific, and a brief account of the peopling of New Zealand. Wellington: AR Shearer.

Brunken, U.; Muellner, A.N. 2012: A new tribal classification of Grewioideae (Malvaceae) based on morphological and molecular phylogenetic evidence. Systematic Botany 37: 699–711.

de Lange. P.J. 2019: Entelea arborescens Fact Sheet (content continuously updated). New Zealand Plant Conservation Network; [accessed 2019 March 4]. http://www.nzpcn.org.nz/flora_details.aspx?ID=1377.

Hare, K.M.; Daugherty, C.H.; Chapple, D.G. 2008: Comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O. suteri; Reptilia: Scincidae) in north eastern New Zealand. Molecular Phylogenetics and Evolution 46: 303–315.

Leach, H.; Stowe, C. 2005: Oceanic arboriculture at the margins – the case of the karaka (Corynocarpus laevigatus) in Aotearoa. Journal of Polynesian Society 114: 7–27.

Moore, L.B.; Edgar, E. 1970: Flora of New Zealand. Vol. II. Government Printer, Wellington

Riley M. 1994: Māori healing and Herbal. Paraparaumu: Viking Sevenseas N.Z. Ltd.

Shepherd, L.D.; de Lange, P.J.; Cox, S.; McLenachan, P.A.; Roskruge, N.R.; Lockhart, P.J.; Kolokotronis, S-O. 2016: Evidence of a string domestication bottleneck in the recent cultivated New Zealand endemic root crop, Arthropodium cirratum (Asparagaceae). PLOS ONE. 11(3):e0152455.

Shepherd, L.D.; Bulgarella, M.; de Lange. P.J.; Chiang, T-Y. 2018: Genetic structuring of the coastal herb Arthropodium cirratum (Asparagaceae) is shaped by low gene flow, hybridization and prehistoric translocation. PLOS ONE. 13(10):e0204943.

Shepherd, L.; Frericks, J.; Biggs, P.; de Lange, P.J. Phylogeography of the endemic New Zealand tree Entelea arborescens (whau; Malvaceae). New Zealand Journal of Botany 57(1): 1–15.

Spencer, H.G.; Brook, F.J.; Kennedy, M. 2006: Phylogeography of Kauri Snails and their allies from Northland, New Zealand (Mollusca: Gastropoda: Rhytididae: Paraphantinae). Molecular Phylogenetics and Evolution 38: 835–842.

Thorsen, M.J.; Dickinson, K.J.M.; Seddon, P.J. 2009: Seed dispersal systems in the New Zealand flora. Perspectives in Plant Ecology, Evolution and Systematics 11: 285–309.

Contact
Associate Professor Peter de Lange
pdelange@unitec.ac.nz

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The stoat genome sequencing project

An important first step has been taken towards assembling and annotating the genome of our most voracious introduced predator, with the capturing of “Stan” the stoat.  Stan, a one-year old male stoat, was live trapped in a cage-trap in the Hikutaia Valley, south of Thames, as part of pest management activities.



Figure 1 Stan the stoat, shortly before dissection.

The stoat genome sequencing project, led by Unitec’s Dr Andrew Veale, will cost over $50,000, and is jointly funded by the Bioheritage Challenge – high-tech pest management solutions, and PredatorFree2050.

What makes Stan special?

There are multiple reasons Stan is the ideal animal for genome sequencing, and searching from him has taken over a year.  So why is Stan special?

Firstly, Stan is a male.

In mammals, males have one X chromosome and one Y chromosome, while females have two X chromosomes.  Therefore, if we want to sequence a Y chromosome, we need a male.  If, however, we were sequencing a bird then we would need a female!

Secondly, Stan’s DNA is in perfect condition.

You can get DNA out of ratty old samples, even ancient bones, so why use a live trapped stoat for this project?

DNA starts degrading as soon as an animal dies.  If you take DNA from an animal that died the previous day, the DNA will still be very good, in pieces probably tens of thousands of base pairs long, but it probably won’t be perfect.  Over time, DNA breaks up more and more, so after a few weeks of decay it will be in millions of pieces, each only hundreds of base pairs long, and ancient samples are generally less than 100 base pairs.

So, to have perfect DNA in complete chromosomes millions of base pairs long, you need a DNA sample as fresh as possible before any decay begins.

Thirdly, there will be minimal contamination.

There is one other factor important to genome assembly, and that is how pure the sample is.  All DNA looks the same, whether it is from a bacterium or a stoat, so contamination from anything else present in the sample will be sequenced at the same time.  Teasing out these contaminated reads of DNA requires intense bioinformatic filtering on the computer.  Bacteria will rapidly increase once an animal is dead.  For a perfect stoat genome, we want to sequence stoat DNA, not bacteria, so again DNA from a fully fresh sample is needed.

Lastly, sequencing a genome requires a low genetic diversity individual.

Assembling a genome is a bit like a giant jigsaw puzzle, but one of the many technical problems along the way is that we all have two copies of this jigsaw puzzle mixed together. This is because we have two copies of each chromosome, one inherited from our father, and one from our mother.  Individuals that are genetically diverse – with distantly related parents, effectively have two different genome sequences.  When the computer tries to assemble these, it looks for overlapping similar sections of reads.  If the two copies are different enough then the computer won’t match them, and it won’t merge them – breaking the DNA sequence.  Do that enough times and instead of having 23 pairs of chromosomes (for a human) or 22 pairs for stoats, we would have hundreds of thousands of bits.  Ideally, therefore we want inbred individuals with low genetic diversity to make it easier for the computer.

While thousands of stoats were introduced to New Zealand, most came to the rabbit filled inland parts of the South Island.  The recorded releases in the North Island occurred near Wellington, and then they spread up the country over the next 20 years.  This means northern New Zealand has lower genetic diversity, and Stan will have a comparatively easy genome to sequence.

What is the process to sequence a genome?

He was taken to a veterinary clinic in a closed dark box with bedding, and humanely euthanized after being sedated.  An ending as comfortable as possible as while he is a pest, he was also an intelligent creature deserving our respect – something too often forgotten by New Zealanders.  His body was then immediately taken to the Applied Molecular Solutions lab at Unitec for dissection.  All organs were removed using sterile techniques like a doctor’s surgery, and immediately frozen to -80°c.  That will keep all of the DNA in perfect condition.

Samples of liver and spleen will now be sent to the Vertebrate Genome Laboratory at the Rockerfeller institute in the USA.

Multiple complex sequencing technologies will now be used to sequence the genome in different ways.  The sequences generated by these different technologies will then be combined on super-computers throughout north America and Europe to create a complete, annotated genome.  If you’re interested in DNA sequencing, and why we need to use so many different techniques, here are some videos detailing the various technologies:

Pacbio Sequencing

Chromium 10x

Bionano mapping

Hi-C

These aren’t even the only ones required to make a ‘platinum’ genome!  It’s a tricky process…

Why sequence the stoat genome?

Current technology will not enable us to eradicate stoats from New Zealand; we need better tools.  Understanding the genome will tell us a lot about stoats, and provide multiple potential ways to help us with their management.

Firstly, it can help us understand stoat population connectivity better – which can then help us plan where and how intense management needs to be.  In his PhD research, Dr Veale evaluated population connectivity of stoats using genetic markers called microsatellites.  On Secretary Island, he showed that stoats were both surviving the intense trapping network (1000 traps over an island about the size of Waiheke), and that they were swimming across from the mainland.  These genetic markers are not very sensitive however, and working out the precise relationships between individuals requires a genome to provide thousands of markers linked to a map.

With a sequenced genome we will also have the sequences for all of the genes relating to olfaction (smell).  Perhaps we can find in these sequences ways to make the perfect lure to attract them?  We will have the genes for immune function, therefore we may also be able to find things that they are sensitive to that could help us control them. There are also possible genomic techniques to control invasive species, such as gene drives.  These technologies are largely hypothetical in mammals, and will require huge amounts of technical research, along with consultation with all the people of New Zealand.

In truth, we don’t know everything that a sequenced stoat genome will give us.  Undoubtedly there are many further unimagined uses for this information to help us understand and control stoats.  This will then help us save our precious taonga species, like kaka, weka, mohua and tieke, which is the whole point of pest management in New Zealand.

“Will all great Neptune’s ocean wash this blood clean from my hand? No, this my hand will rather the multitudinous seas incarnadine, making the green one red.”

 

Contact
Dr Andrew Veale
aveale@unitec.ac.nz

 

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Blog: D’Urville Island stoat eradication planning - Andrew Veale

Blog: D’Urville Island stoat eradication planning – Andrew Veale

This week I went down to French Pass, to help plan the implementation of one of the most ambitious predator eradication programs suggested in New Zealand. This narrow channel separating D’Urville Island from the South Island is possibly the most spectacular (and dangerous) stretch of water in New Zealand, and hopefully it will soon be the moat that helps protect one of our largest predator free islands.

D’Urville Island/Rangitoto ki te Tonga (16,782ha) is the eighth-largest of New Zealand’s offshore islands, and is nationally significant for its diverse geology, relatively intact and diverse plant communities, and high number of nationally-threatened, rare or unusual species. A suite of mammalian pests found on the mainland are absent from the island, including ship rats, Norway rats, brushtail possums and feral goats. Because of the reduced pest suite, the island holds many important populations of threatened species including the New Zealand falcon, marsh crake, giant land snails, skinks and geckos, and in particular it has the largest population of long-tailed bats in the South Island. There are however kiore, mice, stoats and feral cats, which have led to the recent decline of bird species, and the local extirpation of kiwi, kaka and kakariki.

The D’Urville Island Stoat Eradication Charitable Trust (DISECT) was formed in 2004 to promote the concept of stoat eradication on D’Urville Island, and after 14 years of planning and consultation, there is now support from all residents to achieve this goal. If successful this program would make it the largest successful stoat eradication ever attempted in the world.

For me this meeting was not just an opportunity to help plan the project and get a better understanding of the challenges faced here, but it was also a great chance to catch up with old friends and colleagues – many of whom are world leaders in eradication planning such as John Parkes, Dan Tompkins and Peter McMurtrie. For a project this large and complex, every aspect, logistical, ecological and social needs to be planned in detail. Hopefully we will soon publish the results of our discussion to show the reasoning behind the many planning decisions.

So how will this eradication be done?

The residents of the island have opted to do the eradication without toxins – using trapping alone. I should note that I support the use of toxins for many eradications, and that toxins such as brodifacoum are extremely useful and have many benefits, but as the community wishes to attempt this project without their use, this is how we will proceed. It will require traps to be spread across the island at unprecedented densities. Therefore, a dense network of traps is planned, making sure that every stoat home range has at least one trap in it.


Figure 1 Map of the northern half of D’Urville Island showing trap locations surrounded by 350 m buffers.

So let’s say that we can remove all of the stoats, what then?

As MacBeth said “To be thus is nothing, but to be safely thus…” Once the stoats are eradicated, we need to keep them off the island. Stoats are phenomenal swimmers – something I’ve researched in depth, and that is how they arrived on the island originally. While the currents through French Pass are strong, with swirling whirlpools and eddies, obviously they are not enough to keep the stoats permanently at bay. Therefore, the plan is to have traps (and potentially fences) to remove all of the stoats along the potential invasion front. As there is the possibility of stoats swimming up to 5 km, we are planning on trapping all land out to this distance on the mainland.

 

Figure 2 Map showing the putative swimming distances for stoats to the island

One of the important things that we need to do is measure invasion rates to the island – how often do stoats make it across that swirling water? This will help determine how many, and the spacing of traps both on the mainland and on the island. I am currently helping lead an analysis using genetics to see how all of the stoats are related to each other. Once we can look at relatedness patterns among the stoats in the region, we can see how many swim across – basically detecting siblings, parents, aunts, uncles etc on each side. Detecting a relative that swam is much easier than sticking tags on lots of stoats and hoping you catch the one that swims across!

There is still a lot of planning to do, and continuing discussions to be had with the community, local iwi, and funders, but a solid plan is forming that will hopefully lead to a successful campaign to remove these voracious predators. Once they are removed, many endangered species such as rowi, little spotted kiwi and kakariki can be reintroduced. When I started my PhD I had no idea I would spend the next decade of my life helping to apply my research to conservation programs – and getting the opportunity to visit some spectacular places in the process. Cheers to Dave, Andrew, Pip and everyone else involved for inviting me down there!

Contact
Dr Andrew Veale
aveale@unitec.ac.nz

 

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Blog: Climate change, genetics and small fluffy animals - Andrew Veale

Blog: Climate change, genetics and small fluffy animals – Andrew Veale

In my previous position as a postdoctoral fellowship in Canada, I helped a friend of mine Matt Waterhouse, during his PhD work catching (possibly) the cutest animals in the world up mountains.  I also helped out a bit in the lab and with the analyses.  He has just published the research in the top international journal Molecular Ecology, and his research has implications for the future of the species in light of a changing climate.

Figure 1 A pika giving its most threatening expression

 

Pika (Ochotona princeps) are small, nearly spherical relatives of rabbits, that live in the mountains.  They are territorial, and squeak at you when you enter their territory with a sound akin to a little squeaky toy being sat on.  It is dramatically unthreatening to be squeaked at by a little rabbit-like creature puffed up like a furry ball, but they think they are the gangsters of the mountains.  Among their wonderful behaviours are that they gather vegetation and flowers and build haystacks in their little caves as food for the winter – as you can see below.

 

Figure 2 Pika gathering food for its haystack

Unfortunately, they may also be the first mammal to go extinct due to climate change.

Pika live in the mountains in the full alpine zone among boulder fields.  Accordingly, they are cold adapted and temperature sensitive, and their homes in the crevasses between boulders are often covered in snow for most of winter.  With a warming climate they therefore need to go up the mountain to stay in their habitable zone, however mountains have tops, and once it gets warm enough then they will need to live in the space above the mountain – which isn’t easy to do for an animal that can’t fly.  In truth this is an over simplification, climate change has many effects, and many of these effects are not great for pika.  A warming climate may mean decreased snow, which actually can mean their homes get too cold in winter – because without snow as an insulator it gets very cold indeed in their little caves.

What Matt did in his PhD was climb transects up the sides of mountains, catching pika at different altitudes and obtaining small genetic samples from each (from hair primarily, but also little clips off the top of the ears).  This means that the pika remained unharmed and were released back into their caves.  I came up the mountains with him, catching pika and carrying gear and fighting off bears (yes really, there were bears that I had to fight off to get my fair share of the blueberries).

 

Figure 3 Me contemplating the abyss that is climate change

 

He then processed these genetic samples to look for variation within the population.  A SNP (pronounced snip) is a variable site in the genome, where you can have say an A or a T, or a C or a G.  Matt created a dataset with ~31,000 SNPs in it to describe the genetic variation of these pika, and then looked for SNPs that were correlated to altitude.  He found a number of sites on the genome linked with altitude, often near genes associated with metabolism and oxygen transport.  The same sorts of patterns are found in humans, where Tibetans are adapted to live at high altitude while most people are not.  For the pika, there are genetic variants that enable them to live at various altitudes – and these genes vary over very small distances.

He also used migration models (derived from the genetic data) to assess movement and immigration within the pika populations, finding primarily dispersal down the mountains.

All of these findings have important consequences for the adaptation and future of pika.  Genetic variants for each altitude may be lost as their range contracts and habitats change, removing the adaptive potential of the species.  Currently source populations are higher on the mountain, but this may change in the future, and potentially the low habitat between mountains may become unsuitable for them to cross.  Overall his results are not only important for understanding the evolution of pika, but also their conservation management in the future.

For my part I got to help out with an important study and play in the mountains.  Email me on Andrew.j.veale@gmail.com if you can’t get a copy of the paper and I’ll send it along.

 

 

Figure 4 Me releasing a pika after taking a genetic sample

 

 

Figure 5 Matt weighing a pika in a bag

Contact
Dr Andrew Veale
aveale@unitec.ac.nz

 

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A revision of the Sticta filix group

A revision of the Sticta filix group

a rediscovered species, a new combination and the potential for a useful bioindicator of forest health

Lichens are an amalgam of one or more fungi, green algae, cyanobacteria or sometimes both photosynthetic partners. This relationship, a symbiosis, is perhaps best explained as the lichen farming the algae. The algae provide food for the fungus and fungus provides shelter and protection. New Zealand has c.2000 different kinds of lichens, many of which are endemic or now scarce in other parts of the world due to changing climate, air pollution or over-collection by people.

Since 2015 Unitec researchers have been working with an international team of lichenologists on the New Zealand members of the global lichen family the Lobariaceae. The Lobariaceae are a charismatic group of large foliose lichens found throughout the world. Because of their large size they are also widely used for physiological studies of lichen metabolism and as bioindicators of ecosystem health; indeed, one, Lobaria pulmonaria is effectively the equivalent of the ‘lab rat’ as the ideal ‘model organism’ for lichens worldwide.

Lobaria pulmonaria, Sardegna Illorai Forest (Peter de Lange)

New Zealand is recognized hotspot of diversity for the Lobariaceae and as such has become a popular place for their further study. Past research on the family helped resolve the nomenclatural mire of names that had been used for the c.90 or so New Zealand species. Those studies necessarily used lichen chemistry and morphology to help define their taxonomy.

In the last decade there has been a renewed global interest in the taxonomy of the Lobariaceae. For these studies researchers have been using molecular methods to sort out perceived species complexes. Unitec Institute of Technology is a regional hub for lichen research and one of the few tertiary institutions in New Zealand where lichen taxonomy and ecology are taught at degree level. Because of this expertise Associate Professors Dan Blanchon and Peter de Lange from the Environmental and Animal Sciences Department and Applied Molecular Solutions Research Group have been involved with lichenologists Dr Thorsten Lumbsch (Field Museum, Chicago, USA), Dr Robert Lücking (Botanic Garden and Botanical Museum, Berlin, Germany) and Bibiana Moncada (University of Franciso José Caldra, Bogotá, Columbia) on a revision of the New Zealand representatives of the Lobariaceae using a combination of molecular (DNA barcoding using the internal transcribed spacer (ITS) region of the fungus) and morphological methodologies.

One of the groups studied is the Sticta filix group. These are large foliose lichens characterized by having a ‘holdfast’ attachment at the base of the lichen thallus, a dominant green algal partner (photobiont) and a minor secondary cyanobacterial partnership.

Sticta filix, Egmont National Park (Peter de Lange)

The research team has just published a paper in The Lichenologist (Ranft et al. 2018) which has resolved the status of two enigmatic lichens previously referred to the genus Dendriscocaulon – an artificial genus now known to be the result of a ‘failed’ or ‘failing’ partnership in these green lichens, whereby the green dominant partner has been lost, leaving the fungus and cyanobacterial associate to grow independently of its usual green algal partner (as a cyanomorph). When free-living Dendriscocaulon resemble small grey-black or black broccoli. On occasion, the same weird structures can be seen protruding from the base of an otherwise seemingly normal ‘green’ Sticta.  In their paper Ranft et al. (2018) shifted Dendriscocaulon dendroides to Sticta as a new combination S. dendroides because they were unable to discover the green algal dominant Sticta that cyanomorph belongs to. They also showed that the cyanomorph referred in New Zealand to Dendriscocaulon dendriothamnodes is not present. Instead superficially similar cyanomorphs seen here are associated with Sticta latifrons and S. menziesii. As expected Sticta filix also has its own free-living cyanomorph.

Sticta dendroides, Erua Forest, Tupapakukura waterfall track (Peter de Lange).

The second part of the paper revived the name Sticta menziesii. This species had been treated as a synonym of S. latifrons. Ranft et al. (2018) showed that Sticta menziesii is morphologically and genetically distinct from S. latifrons, with which it sometimes grows. They also found that Sticta menziesii has its own unique Dendriscocaulon cyanomorph.

Sticta menziesii, Erua Forest, Tupapakukura waterfall track (Peter de Lange)

The study also noted that Sticta menziesii and S. dendroides were confined to ‘intact’ forested ecosystems. That is these two lichens favoured forests with low possum, goat and deer densities. Sticta latifrons they noted was more common in ‘open’ forest, so it was more often seen in forest damaged by these browsing animals. This research suggests there is potential for Sticta latifrons and S. menziesii to be used as a ‘quick-check’ forest health indicators and is worthy of further study.

Sticta latifrons, Unuwhao Forest, Te Paki (Peter de Lange)

Reference

Ranft, H.; Moncada, B.; de Lange, P.J.; Lumbsch, H.T.; Lücking, R. 2018: The Sticta filix morphodeme (Ascomycota: Lobariaceae) in New Zealand with the newly recognized species S. dendroides and S. menziesii: indicators of forest health in a threatened island biota? The Lichenologist 50(2): 185-210.

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The genomic ancestry of New Zealand’s mice (Part 1)

The genomic ancestry of New Zealand’s mice (Part 1)

New Zealand is filled with the descendants of great voyagers who left their homes in far-off lands for a new life in this idyllic land. This mass immigration has created a diverse melting pot of immigrants from across the world. Along with these human settlers, other, smaller and furrier immigrants also arrived – stowaways hidden away in the supplies below decks… who similarly found New Zealand an irresistible new home.

The first rodent explorers that journeyed across the oceans to New Zealand were the kiore, or Polynesian rat, who travelled alongside the Māori, arriving around 1280 AD. The whakapapa of kiore has helped reveal the routes and timing of the great Polynesian voyages across the pacific. Later, from the 1820s onwards, other rodents including the house mouse arrived hidden away in the supplies of boats coming from all around the world with settlers, sealers, whalers, and traders.

These mice are, like its people, diverse, with whakapapa tracing across the globe. Traces of this ancestry can be uncovered from the DNA of the mice now living here, and from this information we can tell an amazing story of colonization, invasion, replacement, and population mixing.

First, some background on tracing origins through DNA…

We all have two different kinds of DNA in our cells – Mitochondrial DNA which is inherited maternally (only from your mother), and nuclear DNA which is inherited from both parents. Mitochondrial DNA codes for only one process – generating energy in the cells. Nuclear DNA on the other hand, determines everything else about you – how you develop, the color of your eyes and hair, even whether you sneeze when you look at the sun, or if you can smell asparagus urine.

Because Mitochondrial DNA is inherited along one ancestral line without mixing, it is an ideal marker to trace your origins. The majority of scientific research tracing origins using DNA – literally thousands of studies, have primarily focused on mitochondrial DNA. Analyses of human Mitochondrial DNA were the first to suggest the ‘recent out of Africa’ hypothesis, showing that all living humans could trace their maternal ancestry to a single woman living in Africa around 190,000 years ago – a woman who we have christened “Mitochondrial Eve”.

Just like humans, mice have a fascinating diversity of genes, which when analyzed can show how their populations have expanded and evolved. In their native range, the species Mus musculus – better known as house mice, consists of three closely related subspecies with largely separate distributions: M. m. musculus found in Eastern Europe and Northern Asia, M. m. castaneus found in Southeast Asia and India, and M. m. domesticus, native to western Europe, the Near East, and northern Africa. These three subspecies look different to each other (at least to a trained eye) and they are genetically quite distinct, having evolved separately for around 350,000 years.

 

Figure 1. The distribution and colonisation routes of each of the three mouse subspecies. Note that New Zealand has ancestry from all three subspecies.

A few years ago, Professor Carolyn King from Waikato University and I collaborated on a project looking at the mitochondrial DNA of mice in New Zealand. In this study, we found a diverse genetic suite, with a huge diversity of mice from western Europe (M. m. domesticus), East-Asian (M. m. castaneus) mice on Chatham Island and in the south of the South Island, and mice from all three subspecies in Wellington. We found that New Zealand is therefore unique in the world in having all three subspecies introduced, mixing and hybridizing. Hybrids between subspecies are known to have numerous genetic problems, and in particular, domesticus/castaneus hybrids have rarely been studied in the wild due to genetic incompatibilities and non-overlapping ranges. This makes studying the genetics of New Zealand mice extremely interesting.

While we found out that mice had arrived many times, from many places, we still didn’t really know the full story of this complex history of immigration.

Where exactly did all of these mice come from, and how have they mixed since they got here?

We couldn’t answer these questions with mitochondrial DNA alone, so we looked at cutting edge technology recently developed for looking at the mouse nuclear genome. Because mice are a model organism used in biomedical and developmental biology research, cheap genomic marker sets have been developed for analyzing their genomes. We took advantage of these marker sets, and sequenced ~150,000 SNPs for 161 mice from across New Zealand. A Single Nucleotide Polymorphism (SNP) is a change in a single base pair of DNA, and since we were using the same ones that biomedical researchers use there is a wealth of information about the genes responsible for various traits in our data.

What we found was extremely surprising…

The hybrid domesticus/castaneus populations in New Zealand on Chatham Island and in the southern half of the South Island are actually hybrids only in the very limited sense: they have different mitochondrial and nuclear ancestry. Both of these populations are essentially pure M. m. domesticus across the nuclear genome, but they retain the mitochondrial ‘ghosts’ of a previous hybridization event which failed to lead to nuclear genetic mixing in the long term. No traces of their Asian ancestry remain in their nuclear genomes. We had previously thought that these mice had come directly from China, perhaps from sealers returning from the Canton fur markets, but now we can see that almost all of their ancestry came from western Europe!

To put how unusual this in context, it would be similar to you going to the doctor for a genetic test, and being told that one of your mother’s relatively recent ancestors was a chimpanzee – these mice had the wrong mitochondrial genomes!

 

Figure 2. Ancestry plot for all mice sampled in the study. Each mouse is a single column, and the proportion of ancestry to each subspecies is shown by colour. Autosomal DNA is nuclear DNA excluding the sex chromosomes, Mt is Mitochondrial DNA, and the Y chromosome is indicated by Y (for males only).

The spatial patterns of ancestry for mice across the country therefore was therefore completely different from what we had believed given the mitochondrial data!

 

Figure 3. The spatial patterns of ancestry of New Zealand mice, as interpreted from nuclear (autosomal) and mitochondrial DNA.

How could this happen?

Having mitochondria that don’t match the rest of your genome is not as strange as it sounds, because of the different ways the two kinds of DNA is inherited. When an M. m. castaneus mother mates with an M. m. domesticus father, their offspring are 50:50 domesticus/castaneus at a nuclear level, but 100% castaneus mitochondria. If the female offspring were then to mate with an M. m. domesticus male, on average they would be 25% castaneus, 75% domesticus for nuclear DNA, but still 100% castaneus for their mitochondria. After only six generations, they are over 98% domesticus, though still retaining the castaneus mitochondrion. This assumes that survival is even among the offspring, however if hybrids are less fertile or have a higher mortality then those offspring that are closer to ‘pure’ will survive better and re-separation of the genomes can occur even more rapidly.

 

Figure 4. Diagram showing how, after only a few generations after hybridization, you can have individuals that are basically ‘pure’ to one subspecies, but that have the ‘wrong’ mitochondria.

This situation (called mitochondrial capture) would be particularly likely when the original population was small, and when the hybridization asymmetrical, with males of one subspecies mating with female of the other, but not the other way around. These are precisely the conditions that would have occurred on boats or in small founding populations in ports. Previous research has shown that there are severe infertility problems for crosses between mouse subspecies, particularly involving crosses involving male M. m. castaneus. Our findings show that in natural populations, the genomes of these two subspecies are so unstable when mixed, and the fertility of hybrids so significantly decreased, that they re-separate over generations, effectively rejecting the DNA of one of them from the population.

These differences in patterns of ancestry really change how we need to think about how we interpret ancestry based on mitochondrial DNA. We got completely different results trying to assess ancestry based on mitochondrial and nuclear DNA, and hence could not have understood the ancestry for New Zealand mice from only mitochondrial data. Many studies across the world rely on mitochondrial DNA to look at the history of populations, but our study highlights the need to be careful in interpreting these results.

In the next part, we will describe where New Zealand’s mice really came from, and what happened when they arrived.

 

Contact
Dr Andrew Veale
aveale@unitec.ac.nz

 

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Undergraduate student project: One lichen or two?

Undergraduate student project: One lichen or two?

To conserve species we need to reliably be able to identify them, understand their ecology, map their distributions, count their numbers and identify any threats to their survival. Unfortunately, some groups of species are very hard to tell apart, making reliable mapping of their populations difficult. An extreme version of this is the existence of cryptic species, where two independent lineages may be genetically different, but lack obvious morphological differences.

One possible example of this is being studied by Unitec student Marley Ford for his final year research project in his Bachelor of Applied Science in Biodiversity Management. He is studying one of the silver paint lichens – Strigula novae-zelandiae, an endemic species of lichen that lives mainly on the leaves of taraire (Beilschmiedia tarairi) trees in the upper North Island. Previous studies that have looked at taraire leaf samples of Strigula novae-zelandiae have suggested that two different morphological types could be present, possibly representing two different species. Marley is investigating if there are in fact two different species “hiding” under the one name. One morphotype starts as a rounded thallus and gets larger while the other morphotype starts as finger-like lobes which merge to form a rounded thallus.

As well as a traditional microscope study of the lichen in the Unitec herbarium, Marley has been extracting DNA, and using DNA barcoding to compare the different morphological types of this lichen from different locations. Results should be known by the end of November.

 

Contact
Marley Ford
Dr Dan Blanchon
dblanchon@unitec.ac.nz
Dr Peter de Lange
pdelange@unitec.ac.nz

 

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Gannet diet

Gannet diet

Using seabirds to sample marine ecosystems: Australasian gannets in the Hauraki Gulf

 

 

Every MID summer’s day a spectacular, natural phenomenon occurs in the wider Hauraki Gulf namely the departure and return of hundreds of thousands seabirds leaving and then returning to their island breeding colonies to feed their growing chicks. Included in this daily commute is a substantial population of Australian Gannets (tākapu), who spread out across the gulf and then periodically plunge dive on shoaling fish and squid. These fish and squid have often been herded close to the surface by a range of other submerged predatory fish and marine mammals.

This phenomenon and the value of the Gulf for a range of recreational and commercial activities is dependent on the resilience of this coastal ecosystem. All ecosystems are characterised by a complex range of predator-prey interactions represented by food webs. Over time changes in the importance of particular interactions within such webs are likely to reflect the impact of both natural and human related impacts on components parts of these food webs.  Analysing the diet of a range of top predators including seabirds is clearly one approach to providing some indication of the state and health of this coastal ecosystem.

Based on analysis of regurgitate prey from the crop of adult gannets and the stomach contents of squid and fish eaten by gannets, we have made substantial progress towards characterising the range of species that form part of the food web upon which gannets and some other seabirds depend. Identification of primary and secondary prey of gannets has used traditional approaches using visible characteristics of ingested prey and molecular approaches based on the sequencing of the DNA of prey recovered from more digested and excreted food remains. Our results to date have confirmed the general importance of surface shoaling fish, such as jack mackerel and anchovy in gannet diet but also highlighted somewhat unexpectedly for 2017, at least, the northern arrow squid Nototodarus gouldi was an important part of the diet. Analysis of squid and fish stomachs has suggested a central role of a local krill species Nyctiphanes australis in the food web at lower trophic levels.  The diets of the fish preyed on by gannets are more diverse and generally more digested than that of squid. Stomachs have contained, other fish, amphipods, ostracods, decapod and barnacle larvae as well as krill. A more detailed picture of the food web is awaiting completion of further molecular analyses. We intend to repeat aspects of the study in subsequent years to provide some indication of changes in the importance of particular predator prey interactions among years.  Both squid and krill are short lived animals with population size being linked closely to suitable environmental conditions in a given year. Accordingly, population sizes of these species may be subject to large fluctuations between years with implications for gannet diet and foraging behaviour.

 

Collection of fresh stomach samples from seabirds is a time consuming and labour intensive activity.  The demonstration that we could also use molecular analysis of prey DNA on more easily collected faecal samples would suggest a powerful more sustainable approach for longer term studies on gannets and other seabirds. Such longer term studies are important if we are to use this approach to monitor aspects of the health of the ecosystem.

We gratefully acknowledge the support of BirdsNZ in partly funding this research.

The project is a collaboration between: Nigel Adams, Stephane Boyer, Marie-Caroline Lefort, Erin Boyle, Monqiue Wilson, Chloe O’Rouke, Seluvaia Lameko (Unitec) Todd Landers (Auckland Council) and Steffi Ismar (Helmholtz Centre for Ocean Research, Kiel).

 

 

Contact
Dr Nigel Adams
nadams@unitec.ac.nz

 

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Lecanora kohu a new lichen from the Chatham Islands

Lecanora kohu a new lichen from the Chatham Islands

The Chatham Islands group comprise the eastern most extension of the New Zealand Botanical Region. The islands lie 800 km east of Christchurch, and take anywhere from two and half to three hours by plane to reach. The two main islands, Rekohu (Chatham Island) and Rangiuria (Pitt Island) are populated by c.650 people. The main driver of the local economy is marine-focussed, the islands are famous for their crayfish, paua and blue cod. However, sheep and cattle are still farmed, and eco-tourism ventures are on the increase. The biota of the islands is world famous, the islands sporting such treasures as the Chatham Island forget-me-not (Myosotidium hortensia), and black robin (Petroica traversi). Although the fern and flowering plant flora is very well known, data on the islands bryophytes, fungi and lichens is still unavailable.

A DOC ‘Botanical’ Survey was undertaken during the annual mid-winter Chatham Island petrel (Pterodroma axillaris) burrow maintenance that is conducted by DOC staff preparatory to the next petrel breeding season. During the July visit, aside from checking burrows, counting black robins assessing storm damage and undertaking routine weed control and track clearing, it was intended to update the vegetation map for the island, and investigate the vegetation succession within areas of pohuehue (Muehlenbeckia aff. australis) vineland (Fig.1). Oddly Rangatira, despite its global significance as the staging post for the recovery of the critically endangered black robin has had little documentation of its flora. In part this may be because, with an understandable focus on the conservation management of black robin and Chatham Island petrel, most shore parties have been ornithological rather than botanical. That said there has been considerable research effort undertaken to investigate the vegetation succession of the island in the last 20 years. In particular study has focussed on the pohuehue vineland which many bird experts believe is an impediment to the natural forest recovery of the island. Simply put – more forest is needed if we are to have more black robins. To achieve that goal some people wondered if suppressing the pohuehue and planting those areas with forest trees would accelerate vegetation recovery, and so produce more bird habitat?

Critical to answering this question is the need is to determine the current vegetation associations of the island. Without that data, it is difficult to predict the likely future vegetation succession of the island. So, in July 2015 Peter de Lange set out to try and gather that data. Further in addition to vegetation mapping it was decided to update existing knowledge of the islands flora, and also its fungi and lichens – the latter are two life forms rarely noted by scientists visiting Rangatira.

 

Fig. 1. North-eastern portion of Rangatira(South-East Island) viewed from the Trig Station. Much of the flat expanse of vegetation is pohuehue (Muehlenbeckia aff. australis) vineland. Image: P.J. de Lange

 

As Rangatira was once so extensively modified (the island had been farmed), the flora and vegetation of the island though recovering lacks the diversity of that seen in similar habitats on nearby Rangiauria (Pitt Island). Of course, it’s also true that the much smaller size of Rangatira limits the floral diversity – so one would expect less diversity. Nevertheless, following on from the July 2015 survey, and working through the myriad fungal and plant collections housed in New Zealand Herbaria an interim assessment of the flora for Rangatira is that there are 182 indigenous and 68 naturalised fern and flowering plants (including five hybrids and seven (possibly new to science) ‘species’), one hornwort, 28 liverworts (one of which is naturalised to the Chatham Islands) and 50 mosses (including one naturalised to the islands) Four fungi and 119 lichens have also been recorded. Whilst the values for the fern and flowering plant taxa is probably pretty accurate more work is needed for the hornwort, liverwort and mosses – plant groups rarely collected by island visitors. Similarly, there will be more fungi on the island and without doubt many more lichens.

With respect to the lichens, those of Rangatira are, with few exceptions, crustose, often drab species that are easily missed in the gloomy forest. It is only on the exposed coastal cliff faces, shore platforms and rock outcrops of Rangatira that lichens, at least visually, dominate. In particular the white ‘paint’ of Pertusaria graphica forms a distinctive band on the rocks just above the spray zone, and on the islands exposed cliff faces and boulder fields. In places, this is broken by the Dufourea ligulata a species which, depending on the degree of exposure can be yellow, orange or very dark fiery orange. Whilst the rock dwelling lichens of Rangatira are visually conspicuous those of the forest are not; most are scarcely evident, blending with the bark of the trees, shrubs and vines they inhabit. Some are so inconspicuous that they are only seen when the host plant is carefully inspected by torch light or using an ultra violet lamp. There are some occasional surprises though.

One such surprise was found the exposed stems of pohuehue near Western Landing (Fig. 2 and header photo), and again on the bark of mahoe (Melicytus chathamicus). In the field, this lichen presented as a small, whitish crustose ‘scab’. The ‘scab’ on closer inspection sported numerous pinkish depressions (Fig. 2 and header photo). When later examined at the Unitec Herbarium laboratory by Dan Blanchon, thin sections of these immersed pinkish spots revealed that they were fruiting bodies (apothecia) and the spores extracted from these placed the lichen into the genus Lecanora, a species-rich genus of 600 or so taxa. Blanchon extracted DNA from the specimen, and used DNA sequencing in an attempt to place this enigmatic specimen into a known species. The results were more confusing than helpful, placing the lichen within the genus Lecanora, but not matching any known species.

 

Fig. 2. Portion of the type specimen (UNITEC 7497) of Lecanora kohu (left hand side: dry state / right hand side: wet state) showing an example of the new lichen on the branchlet of pohuehue (Muehlenbeckia aff. australis). Image: J.R. Rolfe

 

Images were taken and passed to experts in the USA (Field Museum, Chicago, Michigan State University, Michigan) and Senckenberg Institute, Germany. These elicited sufficient interest that duplicate material was sent to Michigan, and from there to Frankfurt. Initially it was decided that the Rangatira Lecanora was L. confusa, itself of interest as it would have been a new record for the New Zealand Archipelago. Then it was thought the specimens matched an undescribed species from the Falkland Islands. Finally, it was decided that they were in fact a new species.

This odyssey has culminated in the formal recognition of a new species, named Lecanora kohu (‘kohu’ from Te Reo Maori for ‘fog / mist’ in allusion to the sea fog that often obscures Rangatira) (Printzen et al. 2017). The new species is so far only known from the two July 2015 collections made from Rangatira. The species is not present in the other more extensive lichen collections from Rangiauria (Pitt Island) and Rekohu (Chatham Island) but it is probably present there as well. Indeed, any claim to Lecanora kohu being endemic to the Chatham islands would be rather unwise. Previous claims of an endemic Caloplaca, C. maculata, known only from Chatham Island, on coastal cliffs near Waitangi proved unfounded when the species turned up at Akatore, near Dunedin, South Island New Zealand (de Lange 2012). Only time and further collecting will tell whether Lecanora kohu occurs anywhere else in the world.

In the meantime, the discovery of Lecanora kohu on pohuehue and associated mahoe in the regenerating vegetation of Rangatira serves as a pertinent reminder of the need to carefully inventory the biota of a place before deciding on management actions. Currently Lecanora kohu is only known from Rangatira, and we know very little about its abundance, and habitat preferences there. We need more information. Also considering its chance discovery, one wonders what hitherto unrecognised biota also resides within the successional vegetation of Rangatira?

 

Acknowledgements

For assistance in the field on Rangatira during July 2015 Peter would like to thank Bex Bell and James Maunder then staff working for the Department of Conservation Chatham Island Area Office, and Dave Houston, Distributed Technical Advisor, Northern Terrestrial Ecosystems Unit, Department of Conservation. The process of describing Lecanora kohu was undertaken in a series of skips and jumps around the world starting with Thorsten Lumbsch of the Field Museum, Chicago, USA who suggested we follow up the find with Alan Fryday of the Michigan State University, USA and Christian Printzen of the Senckenberg Research Institute, Frankfurt, Germany. We also would like to thank Jack Elix, Australian National University, Canberra, Australia and Robert Lücking, Botanischer Garten und Botanisches Museum Berlin, Germany for offering a constructive review on the paper we subsequently wrote describing Lecanora kohu with Alan, Christian, Dave and Jeremy Rolfe. Jeremy Rolfe kindly supplied the images of Lecanora kohu based on the Holotype lodged in UNITEC.

 

References

de Lange, P.J. 2012: Sole Chatham Islands endemic lichen discovered on south Otago Coastline. Chatham Island New Zealand website. [accessed 2017 August 30]. http://www.chathams.co.nz/index.php/naturalheritage/138-lichen-no-longer-endemic

 

de Lange, P.J.; Heenan, P.B.; Rolfe, J.R. 2011: Checklist of vascular plants recorded from the Chatham Island Islands. Department of Conservation, Wellington. 57pp.

 

de Lange, P.J., Heenan, P.B.; Rolfe, J.R. 2013A. Uncinia auceps (Cyperaceae): a new endemic hooked sedge for the Chatham Islands. Phytotaxa 104: 12–20.

 

de Lange, P.J.; Heenan, P.B.; Houliston, G.; Rolfe, J.R.; Mitchell, A.D. 2013B: New Lepidium (Brassicaceae) from New Zealand. PhytoKeys 24: 1–147.

 

Printzen, C.; Blanchon, D.J.; Fryday, A.M.; de Lange, P.J.; Houston, D.M.; Rolfe, J.R. 2017: Lecanora kohu, a new species of Lecanora (Lichenized Ascomycota: Lecanoraceae) from the Chatham Islands, New Zealand. Submitted: New Zealand Journal of Botany 55. DOI: 10.1080/0028825X.2017.1364274

 

Contact
Dr Peter de Lange
pdelange@unitec.ac.nz
Dr Dan Blanchon
dblanchon@unitec.ac.nz

 

 

Header Photo:  Close up of a rehydrated (wet) thallus portion of Lecanora kohu (UNITEC 7497) showing the distinctive. Immersed ‘pinkish’ fruiting bodies (apothecia). Image: J.R. Rolfe

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Gut microbiome of invasive insects across the Pacific

Gut microbiome of invasive insects across the Pacific

Molecular techniques are being used to investigate how symbiotic microbial communities may be influencing insect invasiveness

For millions of years, New Zealand and the Pacific Islands have been extremely isolated, which has led to the development of native ecosystems with unique biodiversity. But with the increase in human travels and exchanges of goods in past centuries, this isolation is not quite what it used to be.

New species have been arriving en masse, some of which can have devastating effects on native biodiversity and also on agriculture. We call them vermin, pests or invasive species. The ones attacking crops are mainly insects and they can cause millions of dollars of damage to the New Zealand agriculture industry.

Their impact can also be very detrimental to communities whose livelihoods rely primarily on local agriculture and in areas where biosecurity resources are limited, which is the case for a number of Pacific Islands.

“Some species are pests due to the microbes that live in symbiosis in their gut”Lefort

Traditionally, insect pest species are controlled with pesticides. But pesticides may also affect species that are beneficial for crops, such as those that improve the nutrients found in soil or that feed on the pests themselves. It is therefore essential to develop efficient tools to identify these detrimental species and targeted measures to control them before they reach damaging population sizes, but without affecting the non-pest species.

How can we control insect pest species without affecting other beneficial insects?

What makes a species beneficial or detrimental has been the subject of much debate. Here at Unitec, a group of scientists thinks that some species are pests due to the microbes that live in symbiosis in their gut. Most plants produce toxins and other chemicals to deter insects, but pest species still manage to eat and digest the plants. Just like gut microbes help humans digest food, some microbes are helping insects to digest plants. Recent advances in microbiology have highlighted the crucial role of gut microbiome in insect growth, development and environmental adaptation to their hosts.

In the case of invasive insects, it is possible that the contribution of the microbes goes beyond this, and also helps the insect to ‘overcome’ the toxic chemicals that plants produce to protect themselves.

The MADII project

Using modern molecular analyses, it is possible to compare the types of microbes that live in the guts of pest and non-pest insect species. The aim of the MADII project (Microbiome As Driver of Insect Invasiveness) is to use molecular tools to determine the role that gut microbes play in digesting food and handling plant defence chemicals.

What researchers are looking for is a particular set of microbes that would only be present in the guts of pest species and not in beneficial species. If they could identify this ‘invasiveness signature’, new biological control solutions that target those microbes, rather than the insect itself, could be developed. Without their special gut microbes, pest species are likely to be much less of a problem, and this would help reduce the need for pesticides. Such solutions would also ensure the preservation of the biodiversity of beneficial insects occurring in the ecosystem in question.

“Without their special gut microbes, pest species are likely to be much less of a problem, and this would help reduce the need for pesticides”.Lefort

Because Unitec is primarily a tertiary institution, the researchers working on this project wanted it to also be an educational science project. MADII is facilitated through a newly established UNESCO UNITWIN network (University Twinning and Networking Programme) that links New Zealand tertiary institutions with others from the Pacific Small Island Developing States (PSIDS), and aims at enhancing these institutions’ capacities through resources, knowledge sharing and collaborative work in education and natural sciences.

What has been done so far

The project started in January this year with support from Unitec through the Strategic Research Fund. The team comprises eight Unitec staff and students as well as collaborators from three other institutions across New Zealand (Bio-Protection Research Centre, Massey University and Waiariki Institute of Technology) and from the University of the South Pacific in Fiji.

To test the research hypothesis, two model species have been identified and chosen to carry out the study in New Zealand, while collaborators in Fiji are currently investigating the best species model to use in their country.

The invasive Scarab Grass Grub Costelytra zealandica and its close congener but non-invasive species C. brunneum have already been sampled in the North and South Island. The second model comprises the introduced and invasive Black Field Cricket (sampling completed) and the New Zealand native Small Field Cricket for which the team is working at identifying collection sites.

The guts of over 100 of these insects have been dissected and stored at extremely low temperatures to preserve their DNA, while waiting to be prepared for molecular analyses. The team is hoping to get the results from the molecular analyses of the New Zealand species in early September, and those from the Fijian species by the end of the year.

A new website/research platform has also been launched to facilitate the collaboration between New Zealand and Fiji: http://lefortmc.wix.com/madii. Progress on the project can be monitored on the website, and tutorials about molecular techniques and insect dissections will be made available for the general public and to support the learning of the tertiary students involved in the project.

 

Contact
Dr Marie-Caroline Lefort
mlefort@unitec.ac.nz
 

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Assessing chicken welfare using DNA testing

Assessing chicken welfare using DNA testing

Epigenetic DNA sequencing may be used to identify gene expressions of ‘stress’ in chickens

 

How do you know the free-range chicken you buy from the supermarket really had a stress-free life? The answer may actually be written in the chicken’s DNA, and using the right tools, it is possible to decrypt this information.

 

Epigenetics is a relatively new area of study that aims to measure the expression of particular genes in humans and animals in relation to their environment and living conditions. When humans and animals experience stress, hormones called corticosteroids are released in the brain. Long-term effects of stress levels of stress and make changes to brain chemistry which modifies the gene expression that is measurable using DNA sequencing processes. This technology has been used to study the effect of exposure to pollution, drugs, radioactivity, psychological stress and child welfare in humans.

 

It is expected that animals raised in more stressful situations, such as chickens in battery cages, will have a different epigenetic profile than animals raised in less stressful situations, such as free-range environments.

 

Research has already been conducted by animal welfare scientist Dr Jessica Walker and adjunct evolutionary biologist Professor Peter Lockhart revealed that the TPH2 gene, related to the production of serotonin, is more expressed in ‘pecking’ chickens than ‘non-pecking’ chickens.

 

Molecular ecologist, Professor Stéphane Boyer has headed a project with a team of biologists and animal welfare and behaviour scientists, aiming to develop a simple epigenetic test to assess chicken welfare from fresh meat, which could then be used as a commercial testing service. Public opinion has driven a need to consume meat raised in ‘humane’ conditions; consumers want to know that their dinner did not ‘suffer’. In addition, for New Zealand producers to quantify the welfare of their chickens on a world standard has the potential to increase New Zealand’s credibility as a supplier and the international demand for humanely-raised, free-range chickens.

 

This project is a first look at studying animal welfare from an epigenetic point of view and fits well into Unitec’s research foci. Current research will study meat from commercial outlets and future research will study live animals in a range of captive environments.

 

Contact
Dr Kristie Cameron
kcameron@unitec.ac.nz
Professor Stéphane Boyer
sboyer@unitec.ac.nz

 

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The power of pathogens

The power of pathogens

The power of pathogens: Unitec scientists and students have been researching natural herbicides to control an invasive weed that threatens New Zealand’s native ecosystems.

Research on natural enemies of the invasive African club moss (Selaginella kraussiana) is helping to protect New Zealand’s native ecosystems, while enabling Unitec students and graduates to undertake industry-generated research. Led by Dr Dan Blanchon, Associate Professor and Head of Environmental and Animal Sciences at Unitec, and Dr Nick Waipara, Auckland Council’s principal advisor of biosecurity, students and graduates have been investigating possible natural pathogens of the invasive introduced plant. The hope is to find a fungus which could be used to create a mycoherbicide (fungal herbicide) that would help to control the plant, which originates from Madagascar and other wet areas of Africa.

Through DNA testing of approximately 100 fungi found on discoloured or wilted leaves of the club moss, two promising fungal isolates have emerged as natural enemies of the club moss. There are a number of fungal isolates still to be tested, with the hopes that an even stronger candidate will be found. “In an ideal world, we’re looking for something that really kills or knocks back the club moss but doesn’t attack anything else,” explains Blanchon.

African club moss is common in Auckland and Northland, but the Department of Conservation is now seeing it spread further, including into parts of the West Coast. The plant establishes itself in shady, damp environments, spreading along tracks and into the bush on people’s boots, through rainwater and through its own spores. “It is going to be a pest of national significance,” Waipara says.

The research project was initially commissioned by Auckland Council in 2011, with the aim of finding a biological control for the invasive plant, as per their current pest management strategy. If one can be found locally, it will save having to look overseas to the plant’s original environment. This would be an expensive exercise and potential risks are involved if another species was to be introduced to New Zealand.

Waipara asked Unitec to look at the impacts of the African club moss plant on the native environment and to explore possible solutions to these impacts. Though the weed and its negative effects were known, biological control research had not been undertaken in New Zealand or overseas, causing the weed to be overlooked in many pest management programmes. “This weed is an issue for northern New Zealand and hasn’t had a lot of research around it,” he explains.

The plant is hard to control, as it creates thick layers of ground cover, which smother native plants and seedlings. Using general herbicides would kill these seedlings, mosses, ferns and lichens as well as the African club moss, which would return at a faster rate than the native species and inhibit their growth. “What you really want is to target this [club moss] specifically,” explains Blanchon.

The tools that the Council can use against the plant are limited, and being able to combine biocontrol with chemicals and hand removal would help, says Waipara. “The more armoury you have against some of these pests the better.”

With a background in scientific research himself, Waipara has been collaborating with Blanchon and students on the research. The Council runs a biosecurity studentship summer programme with Unitec, and initially funded summer student Hayley Nessia to undertake research, followed by other students and graduates, including Matt McClymont, Christy Reynolds, Sarah Killick and Orhan Er. Impact studies conducted showed that the plant had an invasive impact in the native ecosystem, including suppressing seedling growth, and causing a significant decrease in the abundance of native plants.

The next stage involved looking for pathogenic fungal isolates to reduce these impacts. Samples of unhealthy-looking plants were collected from areas of Auckland and Northland, including parts of the Waitakere and Hunua Ranges, Whangarei and Waiheke Island. These were screened in the Unitec laboratory for fungi. A sample of each fungal isolate was taken and identified through a number of processes, including DNA sequencing through Massey University. These fungal isolates were reapplied to damaged and undamaged samples of the club moss, to check for pathogenicity. Two promising pathogens emerged, including Phoma selaginellicola, which attacks African club moss significantly but does not kill it however, as it seems to be specific to African club moss, the bonus is that it would not kill other plants if used as a mycoherbicide. The other candidate is Pestalotiopsis clavispora, though it is more of a ‘generalist’, says Blanchon, so other plants could be at risk if it was used as a biocontrol agent.

Whether or not the pathogenic fungi would be successful as biocontrol agents in the field has not been determined yet. The project is nearing completion, and soon, Blanchon and his team will submit recommendations to the Council. If they have found an isolate that shows enough promise as a biological control, the Council may look to develop this as a mycoherbicide. A number of trials would need to be conducted to ensure it is safe, and to gauge any potential adverse effects on native club mosses and other native species If none of the fungal isolates are suitable as a biocontrol, the next phase may involve the Council going offshore. Other options include taking an integrated approach, says Blanchon, such as spraying an initial low-dose herbicide followed by a mycoherbicide that would hopefully kill the weakened African club moss. “The low-dose herbicide would weaken everything, but the native stuff should recover,” he explains.

Whatever the outcome, Waipara says Unitec’s research has been critical in helping the Council to determine their next step. It has been beneficial for Unitec as well, says Blanchon, with students and graduates getting to work on a real-life research project which combines biodiversity with biosecurity. They have also had the opportunity to be hired as researchers and to contribute to a number of published studies.

 

Contact: Dr Dan Blanchon dblanchon@unitec.ac.nz

Dr Nick Waipara Nick.Waipara@aucklandcouncil.govt.nz

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Conservation of the 'unfashionable': the use of DNA sequence data to identify our neglected biodiversity

Conservation of the ‘unfashionable’: the use of DNA sequence data to identify our neglected biodiversity

Our knowledge of the biodiversity of New Zealand is unevenly spread. Charismatic or larger organisms such as birds, reptiles, fish and higher plants are generally well known and well-studied. We do however have more neglected corners of our biodiversity.

For a range of reasons some taxonomic groups have not been as extensively studied as the better-known groups of organisms. There may be few or no experts in that field in New Zealand; the organisms may be microscopic, have cryptic distinguishing characteristics, or may live in inaccessible places and environments. These neglected taxonomic groups, such as fungi and many groups of invertebrates, are thought to represent a significant part of our native diversity. Some of them may be threatened with extinction, but without knowing anything about them, it is rarely possible to even attempt to manage them.

Dr Peter de Lange is a Principal Science Advisor at the Department of Conservation (DoC) and a research fellow at Unitec. He collaborates with Dr Dan Blanchon from Unitec’s Applied Molecular Solutions Research Focus on a range of projects studying lichenised fungi, or ‘lichens’.

“Lichens are a significant part of New Zealand’s biodiversity, but they are poorly studied, poorly known. We are beginning to understand that they are very important bioindicators of climate change and changing forest structure and health. Because we often don’t know what species we are dealing with, we can’t effectively manage them – we need to know what we are dealing with. DoC is increasingly broadening its approach to include all forms of life in New Zealand, including more cryptic things like lichens,” says de Lange.

The last full review of the lichen species in New Zealand, started in 2009 and published in 2012 by a DoC threat classification panel, recognised 1799 different lichens and associated fungi as being found in New Zealand. The purpose of this review was to determine if any lichen species were threatened with extinction. It turned out that more than half of the species were so poorly known that they were listed as ‘Data Deficient’, and therefore could not be assigned to a threat category.

In 2016, a new threat classification panel for lichens (led by de Lange and including Unitec’s Dr Dan Blanchon) will meet again to determine the threat status for New Zealand’s lichens. The task is a daunting one, as conservative estimates now suggest we may have as many as 2500 different lichens and associated fungi in New Zealand.

“A large proportion of New Zealand lichens are considered to be ‘Data Deficient’ – in some cases we are not confident that they are actually real species,” says de Lange.

Part of the solution lies in the judicious use of molecular technologies such as DNA sequencing. While there are few active lichenologists in Australasia, worldwide there are several laboratories working on different lichen genera and families, many of which are represented by species in New Zealand. Their work, and research carried out in the Applied Molecular Solutions laboratory at Unitec by Blanchon, de Lange and Dr Sofia Chambers involves extracting DNA from lichen specimens, generating DNA sequence data and comparing this with other published sequences available in online databases. A vast amount of genetic data is available for comparison on international databases such as Genbank.

 

“Lichens are very important bioindicators of climate change and changing forest structure and health.” de Lange

 

“Lichens are a little odd to work with, as they are actually communities of organisms, made up of a fungus, which ‘farms’ captured algae and/or cyanobacteria. In practice, the scientific name of the lichen refers to the fungal partner, and it is the DNA of the fungus which is usually compared,” says Blanchon. Comparison of DNA sequences can uncover or identify species new to science, confirm or dispose of species names and help us to understand the relationships between or within species worldwide. “DNA is the only reliable way of getting to grips with problematic groups – getting unknown taxa down to at least genus level. When studying lichens, without getting DNA sequence data you are dreaming if you think you are going to do a good job,” says de Lange.

Blanchon and de Lange are collaborating on a range of lichen projects, most involving the use of DNA sequence data. One interesting project involved a hunt for a mysterious ‘missing’ lichen called Ramalodium dumosum. This lichen had only been collected once (in 1981), by a collector called John Bartlett, from coastal cliffs at Huia near Auckland and was never seen again.

A thorough survey of the Manukau Harbour coastline (including an accidental discovery of a nudist beach) uncovered one possible candidate for the elusive R. dumosum. This unappealing microscopic gelatinous black lichen was taken back to the lab for DNA analysis. Comparison of the ITS DNA sequence data with Genbank sequences indicated that this specimen was actually a new species of Enchylium rather than Ramalodium, replacing one mystery with another.

Another example of the value of molecular data is from the Chatham Islands (Rekohu). Rangatira (South-East) Island is the site of an attempt to restore population numbers of the critically threatened Chatham Island Black Robin. The succession of the native plant pohuehue (Muehlenbeckia australis) had been identified as a possible barrier to the Black Robin recovery programme on the island. However, before removing the pohuehue, it was important to determine if there would be negative effects on other species. A lichen was collected from the pohuehue by de Lange, and an examination back in the lab at Unitec suggested it could be a new species. DNA data has subsequently shown that it is indeed a species previously unknown to science.

The use of molecular data can also cause surprises with common lichen species. Blanchon hosted a Royal Society of New Zealand Teacher Fellow, Glenys Hayward. Hayward and Blanchon studied the common and widespread lichen Ramalina celastri, a species found in virtually every backyard in Auckland. In Australia, the species was separated into two subspecies, but in New Zealand we only recognised one species.

Comparison of DNA sequence data from specimens collected from New Zealand and Australia showed that we should recognise two separate species, R. celastri and R. ovalis (an old name for specimens mainly found in the South Island of New Zealand and eastern Australia), adding one species to the total known lichens for New Zealand.

In addition, collaboration in worldwide studies can show that in some cases where we previously thought we had species with a worldwide distribution, we are wrong.

For example, at Unitec we are part of the PARSYS consortium, investigating members of the family Parmeliaceae all over the world.

 

“A common species around Auckland that we have been calling Parmotrema perlatum is not in fact that species.” Blanchon

 

We are currently revising the species of the genus Parmotrema for New Zealand. Initial results are indicating that a common species around Auckland that we have been calling Parmotrema perlatum is not in fact that species. The species with this name has been listed as a culinary herb in places such as India – and based on our data, what we have here is not that species, which appears to be restricted to the Northern Hemisphere.

One essential step in the use of molecular tools such as DNA sequencing for studying lichen species is in the creation of voucher specimens – the preserved sample of the lichen the DNA was taken from, lodged and protected for posterity in a collection such as a herbarium.

The DNA sequence data is linked to the collection number of the specimen and this specimen can be checked by other scientists – such peer review is an essential part of the scientific process. Voucher specimens substantiate claims of occurrence and can provide useful information on the geographical distribution and ecology of species.

“Unitec is the only lichen-specialist herbarium in New Zealand,” notes de Lange. “Some other herbaria maintain lichen collections, but they may not have specialists working there or may not be actively adding to or curating their collections. Unitec provides a specific type of service to the New Zealand people that none of the other New Zealand herbaria do.”

Pullquote: “Voucher specimens substantiate claims of occurrence and can provide useful information on the geographical distribution and ecology of species”

With between 1800 and 2500 lichens to choose from, the list of projects for the Unitec and DoC researchers is nearly endless, but every puzzle they solve is a win for our understanding of New Zealand’s biodiversity.

 

Contact
Dr Peter de Lange
pdelange@unitec.ac.nz
Dr Dan Blanchon
dblanchon@unitec.ac.nz

 

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Molecular analysis assists restoration project

Molecular analysis assists restoration project

A study of the native carabid’s diet is helping to enhance the beetle’s chances of survival in new habitats

 

For three years, Unitec’s Dr Stephane Boyer has been analysing the diet of native carabids (Megadromus guerinii) found on Christchurch’s Banks Peninsula. The science lecturer’s findings have provided essential knowledge for the restoration of Ōtamahua/Quail Island, and will aid in the understanding of native beetles, including their role in food webs and function in New Zealand native ecosystems.

Carabid beetles play an important role. The predatory insects help to contribute to soil fertility, vegetation renewal and weed control, and provide a food source for other animals. Boyer’s diet analysis, funded by the Brian Mason Trust, aimed to determine why 44 of the black flightless beetles, native to Banks Peninsula, did not survive translocation to Quail Island. After molecular analysis of the carabid’s faeces, Boyer has determined that the hypothesised lack of food on the island was most likely not responsible for the beetle’s inability to survive. “We found that the native ground beetle feeds on a wide variety of insect larvae including flies, other beetles and moths, many of which are present on Quail Island,” he says. “Therefore, reasons for the disappearance of the translocated individuals are unlikely to relate to inappropriate food.”

His study was part of an ongoing restoration project on Quail Island. The small island, inside Lyttleton Harbour on Banks Peninsula, was home to the now extinct New Zealand Quail and a number of other species, before the land was cleared by Maori and European settlers. The 85ha recreational reserve, administered by the Department of Conservation (DoC), has been the focus of restoration efforts for the past 20 years by the Ōtamahua/Quail Island Ecological Restoration Trust, in partnership with DoC and Te Hapu o Ngāti Wheke of Rāpaki.

“The main aim of the Trust was to facilitate the restoration of indigenous vegetation and fauna on Ōtamahua/Quail Island and provide refuge for locally extinct or rare and endangered species of the Banks Peninsula region,” trustee and Lincoln University ecologist Mike Bowie explained in his 2008 paper, Ecological restoration of the invertebrate fauna on Quail Island (Ōtamahua). With help from a number of volunteers, the Trust has attempted to restore the island to its pre-human state, through the replanting of over 100 species of native plants and controlling invasive predators, such as deer, possums and rats.

Although the island is now largely predator-free (apart from mice, which are difficult to eradicate), it has been hard for native species to recolonise the reserve, due to it being an island. As Boyer explains, “although the new conditions have prompted the return of a number of birds, such as bellbirds and kereru, and penguins are now nesting on the island, Quail Island remains out of reach for many other native animals that would have likely lived on the island prior to human arrival.” Bowie, Boyer’s former Lincoln University colleague, has been on the Quail Island Trust for over 15 years, and has been instrumental in reintroducing native species to the island. “On Banks Peninsula there are roughly 50 [species of] carabid beetle, whereas on Quail Island there are probably only about five,” Bowie explains. “The ones we are particularly interested in are the Banks Peninsula endemic species.”

“The predatory insects help to contribute to soil fertility, vegetation renewal and weed control, and provide a food source for other animals”Boyer

The Trust reintroduced a number of these carabids, along with weta and leaf vein slugs. These were collected from Banks Peninsula and transported to Quail Island in weta motels – hollow wooden containers which the weta crawls into – and wooden discs, which carabids naturally inhabit. “These artificial shelters were also used to monitor the survival of the animals after release,” says Boyer. “Although most translocations were successful, there is one particular case where 22 male and 22 female native ground beetles were reintroduced, but none could be recovered after a year.”

Bowie enlisted Boyer’s help with this issue, knowing he was well qualified for such research, his PhD having focused on the ecology of invasive and native cockroaches on two French islands in the Indian Ocean. Much of Boyer’s other work has focused on invertebrates, and the conservation of native species.

With predators largely eradicated, Boyer thought a possible explanation for the carabids’ death was the lack of appropriate food on the island. To ascertain the exact contents of their diet, with help from students, carabids were collected from Banks Peninsula. These were placed in petri dishes lined with paper towels. The beetle’s faecal matter was then collected and analysed, and the beetles returned to their original location. Initial samples provided insufficient data, so experiments were repeated the next year. Former post-doctoral student Dr Richard Winkworth helped with the more complex sequence analysis. “This [data] was analysed using next-generation DNA sequencing methods,” explains Boyer”.

“This allowed us to identify which prey were eaten, from the DNA traces that remain in the faeces of predators after digestion.”

Boyer says he was not entirely surprised at the range found in the carabid’s diet. After discovering that the prey species of the carabid were largely available on Quail Island, diet was ruled out as an issue in their survival.

The next hypothesis is that the lack of habitat available on the island was responsible for their inability to thrive. Carabids nest under old pieces of wood or rotting tree trunks, and there are not a large number of these on the island.

While Boyer is not involved in this phase of the project, including the next attempt at translocating carabids, he plans to make recommendations relating to their habitat, such as leaving more wooden discs to rot on the island. These will mimic dead tree trunks and provide safe havens from mice, possible predators of the beetles. Boyer also recommends using the same diet analysis techniques in future restoration projects.

“The molecular protocol developed for this study is applicable to other carabid beetles and other invertebrate predators in general,” he explains. “It is advisable to conduct this sort of analysis prior to the translocation of endangered species in areas outside of their current distribution.”

contact
Dr Stephane Boyer
sboyer@unitec.ac.nz

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The plight of the whitebait

The plight of the whitebait

The closing of a reportedly “lacklustre” whitebait season has New Zealand scientists speculating on whether the industry is sustainable.

They’ve called for whitebaiters to be licensed and the banning of commercial harvesting.

“There is no doubt that freshwater fish populations in New Zealand are declining,” says Dr Mike Hickford, research associate at the University of Canterbury’s marine ecology research groups.

“But there is no evidence to link this to whitebaiting.”

He says the main problem with addressing the issue is no-one has comprehensive catch data so no one has an idea what the longer term trends are.

Mike suggests a whitebaiting licence much like a Fish and Game Sports Fishing Licence.

“Whitebaiters would buy a licence for a set number of days and would have to nominate rivers and regions.”

The fee would support research and compliance. But the major benefit would be data on people fishing and when and where – basic data crucial for managing a fishery.

Dr Stephane Boyer, senior lecturer Environment and Animal Sciences at Unitec says white baiting practices aren’t sustainable.

“One of the big issues is we don’t know what species we catch. There are five species of fish but as babies they all look alike. Three of the five species are declining and one is recognized as threatened. Yet we fish, eat and sell without distinction.”

Stephane says it’s certain we are not getting any less effective at catching whitebait. “So a drop in the total catch can reasonably be imputed to a drop in the population of juveniles.”

There’s a dire warning from Dr Mike Joy, senior lecturer in environment science/ecology at Massey University.

“Whitebaiting is a really important thing for New Zealanders. If we don’t fight to save this right, if we don’t do anything about the habitat loss and pollution and commercial harvesting, then we’re going to lose it.”

Stephane says we do know the number of adults is declining and their distribution is reducing.

“We should give native fish the same protection as trout and, in the short term, ban commercial harvesting in order to reduce the pressure on juvenile whitebait.”

contact
Dr Stephane Boyer
sboyer@unitec.ac.nz

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Future-proofing the Petrel

Future-proofing the Petrel

Molecular analysis of the Westland Black Petrel’s diet is aiding in the conservation of the small population of rare birds

Unitec senior lecturer Dr Stephane Boyer is intent on ensuring the survival of the Westland Black Petrel/Tāiko (Procellaria westlandica). For two years, he has been utilising molecular analysis to detail the bird’s diet during the critically important breeding season.

Westland Black Petrel / Tāiko (Procellaria westlandica)Paparoa National Park, Punakaiki

By collecting and analysing non-invasive DNA samples, with help from undergraduate research students, Boyer has been aiming to determine whether the species is still heavily reliant on waste from the fishing industry, as was discovered in a 1998 Lincoln University study by Amanda N. D. Freeman.

The rare bird, which is native to the West Coast of New Zealand’s South Island, is classified as vulnerable by the International Union for Conservation of Nature. If care is not taken to manage its fragile habitat, food supply and the threat of predators, it will risk extinction.

There is an estimated annual breeding population of just 3000-5000 pairs of Petrels.

They fly as far as South America and Australia in the summer and, in winter, return to nest in an area of forest in the Paparoa National Park, south of the tourist hotspot of Punakaiki.

It is the only place in the world where they nest, therefore conserving the area and its birdlife is crucial. The birds bring visitors to the area, with one tour company offering sunrise and sunset tours for those who have travelled from around the world to witness the ‘return of the Petrel’.

Boyer’s research began when he was working at Lincoln University, helping the group Conservation Volunteers to restore and maintain the Petrel’s habitat. This involved replanting vegetation and ensuring that no major development, mining or building would occur in the area.

By finding out the exact contents of the bird’s diet, their food supply could also be monitored. Boyer’s prediction was that he would find different species in the bird’s diet than those found in 1998, due to changes in both the environment and the fishing industry over the last 18 years.

“If care is not taken to manage its fragile habitat, food supply and the threat of predators, it will risk extinction”Dr Stephane Boyer

“I’m interested to see what has changed, whether [the birds] are shifting to something different, whether they are still very much dependent on this fishery waste,” he explains.

“Due to uncertainty in future sea-surface temperature, sh stocks may vary greatly from year to year, which could decrease fishery waste, thereby impacting adult survival during the breeding season.

“In a recent study by Te Papa staff, Susan Waugh found that the main driver of Westland Petrel population growth was adult survival during the breeding season, with hoki fishery catch being a good predictor of adult survival.”

While a four-fold increase in the amount of hoki caught in the area may have increased the bird’s dependence on fishery waste, improvement in fishing practices and
regulatory changes may have lowered the quantity of waste, and future regulatory changes could lower this even further. Since the 1998 study, more advanced collection and analysis methods have enabled a more detailed picture to be taken.

“The diet analysis method used in 1998 required forced regurgitation and could only apply to relatively intact pieces of flesh or skeleton,” Boyer says. “The results, therefore, represent an only partial picture of the Petrels’ diet. We now have much better analysis tools and protocols, so we don’t even need to approach the birds. It is possible to draw a much more accurate and detailed picture of the birds’ diet, including detecting all prey species predated by individual birds.”

Because the birds are at sea during the day, Boyer was able to collect faecal samples from the entrance of their burrows, without disturbing the nests or the birds themselves.

Samples were taken in April and September, the start and end of the nesting season. Boyer hopes to determine what is being fed to the chicks, and what the adults are eating during the incubation period. “That will give us a much bigger picture of what they eat as a species,” he says.
The DNA samples have undergone molecular analysis in the Unitec Applied Molecular Solutions laboratory, followed by next-generation sequencing analysis at New Zealand Genomics Ltd.
Preliminary findings, based on an initial pilot study, show that while the bird’s diet has changed since 1998, it is still largely made up of fishery waste, with 44 species of fish and octopus present. The second, larger set of samples is currently being analysed, with final results expected in June.

contact
Dr Stephane Boyer
sboyer@unitec.ac.nz