Dec 022016
 
Some of the herbarium collections of Marchantia held in the RBGE herbarium

Some of the herbarium collections of Marchantia held in the RBGE herbarium

Many new species are already included in natural history collections around the world, it’s just that nobody has yet got around to examining the material, recognising that it represents something novel, and publishing a name for it. Sometimes these new species are filed under the epithet of a similar named species, sometimes they’re just filed under the genus name with other collections that have not been identified to species, and sometimes they have been annotated to recognise that they’re probably distinct from all the species that have already been described, e.g., as “sp. nov.

David Long has made a huge number of plant collections from around the world in his 40-plus year botanical career, with many of these collections not yet fully examined. Some of this material is being mined for DNA sequencing projects at RBGE, and for some of our key plant groups, as well as sequencing well-identified material, we are also sequencing plants that have not been assigned to species. Molecular lab work is fast compared to close morphological studies of multiple plant specimens; this can therefore speed up the processes of traditional taxonomy, by allowing it to focus on things that are obviously distinct.

One lineage that David Long is particularly involved with, and that remains one of our key plant groups, is the complex thalloid liverworts. Some of our sequencing work has involved Marchantia, which made Xiang et al.‘s recent description of a new species in the genus, Marchantia longii, particularly interesting. In the last few days, the DNA sequences that were included in the paper were made publicly available on the NCBI site, GenBank. One of the regions that was sequenced by Xiang et al., the plastid-encoded RuBisCo Large subunit gene rbcL, was also included in our study, and so I was able to put the two data sets together, and see how the new species fits into our phylogenies.

The results are interesting: When Xiang et al. named M. longii, they did so in part because the area that the plant came from, in northwestern Yunnan, is one in which David has been very active. In fact, at RBGE we had already generated DNA sequence data from nine accessions of Marchantia that David had collected there. I was delighted to find that two of these accessions (collections Long 36155 and Long 34642), which had been filed in our collections without a specific epithet, are an exact genetic match to Marchantia longii. It seems that David really does have an affinity for the plant, having gone out and found some even before it was named for him!

 

Long’s Marchantia

A rapid phylogeny of Marchantia, from the RBGE collections. II. Illuminating our sampling

A rapid phylogeny of Marchantia, from the RBGE collections. I. Sampling

Nov 222016
 
David Long in Gaoligong Shan; photo by Dong Lin

Dr David Long in Gaoligong Shan; photo by Dong Lin

Formerly the head of our Cryptogam section, and currently an extremely active RBGE Research Associate, David Long is well known and respected for his botanical work in the Himalayas, and for his bryological research. He has collected a huge number of taxonomically and phylogenetically interesting bryophytes on numerous plant collecting expeditions, collaborating with researchers around the world. His 2006 monograph on Eurasia Asterella reflects a special interest in the complex thalloid liverworts (Marchantiopsida), which has formed a focal point for subsequent research at RBGE on the systematics of the group (e.g., Villarreal et al. 2015).

Marchantia longii, from Fig. 1, Xiang et al. 2016, The Bryologist

Marchantia longii, from Fig. 1, Xiang et al. 2016, The Bryologist

In October this year, Chinese colleagues You-Liang Xiang, Lei Shu and Rui-Liang Zhu, using morphological and molecular evidence, described a new species of Marchantia from the northwestern region of Yunnan. Their paper, in the American Bryological and Lichenological Society journal The Bryologist, suggests that this is a distinct species, phylogenetically related to Marchantia inflexa, M. papillata and M. emarginata.

Xiang et al. 2016, The Bryologist

Fig. 4, Xiang et al. 2016, The Bryologist

The new species differs morphologically from other Marchantia species in the area by a suite of pore, thallus and receptacle characters, one of the most obvious of which is its very large epidermal pores, which can clearly be seen in the photographs presented by Xiang et al. The authors have named their new plant Marchantia longii R.L.Zhu, Y.L.Xiang et L.Shu, in honour of David, because he is “the specialist of complex thalloid liverworts and made several bryological expeditions in northwestern Yunnan, China”.

On these expeditions to the area, David collected extensively. It remains to be seen, however, whether his own collections include any plants of the newly named Long’s Marchantia!

Nov 162016
 
Telaranea tetradactyla, photographed by David Long (Long 37778)

Telaranea tetradactyla at Benmore, photographed by David Long (Long 37778)

Murphy’s threadwort (Telaranea murphyae) has had a singular position in the British flora. The species was described by renowned bryologist Jean Paton in 1965, from plants collected in the south of England. It’s a tiny leafy liverwort that is found in only four locations, at Tresco and St Mary’s on the Isles of Scilly, Branksome Chine, Poole in Dorset and Alum Chine, Bournemouth. Murphy’s threadwort has always been known to be an alien species in our flora, and yet because it’s never been found elsewhere, the sole responsibility for conserving the species lay with the UK. Being non-native, however, it was not considered a priority for UK Biodiversity Action Plans.

Telaranea tetradactyla from the RBGE fern house, photographed by Lynsey Wilson

Telaranea tetradactyla from the RBGE fern house, growing with Conocephalum conicum; photographed by Lynsey Wilson

Using DNA sequence data from the plant, and comparing it to sequences from other related species, we showed that genetically, the English plants are the same species as a New Zealand plant, Long’s threadwort (Telaranea tetradactyla, synonmy Telaranea longii). Long’s threadwort was already known from several locations in the UK, including inside the fernhouse at RBG Edinburgh, and near the fernery in Benmore. These habitats are not entirely coincidental – the Victorian craze for ferns saw many gardens import living tree ferns from countries such as Australia and New Zealand, with many smaller plants hitching a ride along on their trunks. Today, conscious of plant health issues and the potential transport of pathogens, new plant living collections have to spend time in quarantine before being planted out; past gardeners were less careful, and some of these hitchhikers have subsequently escaped into the local landscape.

Telaranea tetradactyla from the RBGE fern house, photographed by Lynsey Wilson

Telaranea tetradactyla from the RBGE fern house, photographed by Lynsey Wilson

Sinking our UK Murphy’s threadwort plants into the New Zealand species means that any conservation requirements now rest instead with New Zealand, although we can continue to enjoy seeing this diminutive mat-forming liverwort in its select few UK locations.

 

 

Key reference: Porley, R.D., 2013, England’s Rare Mosses and Liverworts. Princeton University Press.

 

 

Villarreal et al. 2014, Journal of Bryology 36(3): 191-199

Villarreal et al. 2014, Journal of Bryology 36(3): 191-199

 

Sep 142016
 
Sphaerocarpos texanus and S. michelii, from the British Bryological Society Field Guide (see references for link)

Sphaerocarpos texanus and S. michelii, from the British Bryological Society Field Guide (see references for link)

In conjunction with Dr Daniela Schill’s monographic work on Sphaerocarpos, we’ve been building a molecular phylogeny for the genus. We have attempted to extract DNA from 66 accessions, including three S. cristatus, all from California, seven S. donnellii from the US, five S. drewei from California, two S. hians, 13 S. michelii from France, Great Britain, Italy, Malta and Portugal, two S. muccilloi, five S. stipitatus from Nepal, Portugal and South Africa, and 25 S. texanus from Belguim, France, Great Britain, Italy, Portugal, Turkey, California and Illinois. We have also included some as yet unidentified material, including an accession from Chile.

Because much of our work at RBGE focuses on plant DNA barcoding and the protocols are established and frequently successful, we have chosen to use sequence data from some of these barcoding regions for this project. However, the liverwort matK primer sets were not very successful in Sphaerocarpos, with a very limited number of good quality sequences generated. The nuclear ITS2 region had its own issues, with many of the sequence reads being difficult to interpret due to overlapping peaks. In the end we focused on the three most successful plastid loci, the rbcL and rpoC1 barcoding amplicons, and a region that encompasses part of the psbA gene and the psbA-trnH intergenic spacer.

Unfortunately, we have not been able to amplify DNA from all the samples we extracted, with failures particularly for some of the older specimens. One of the species we attempted to sequence, Sphaerocarpos muccilloi, has not worked for any of the gene regions that we have been using, while another species, Sphaerocarpos hians, has so far only amplified for a single region, rbcL.

Sample phylogenetic tree for Sphaerocarpos, based on rbcL sequence data

Sample phylogenetic tree for Sphaerocarpos, based on rbcL sequence data

Although each species seems to be genetically distinguishable from the other species sampled, two of the most widespread species, S. michelii and S. texanus, are resolving as para- or polyphyletic. The phylogenetic tree contains three distinct groups of S. michelii accessions, and two distinct groups of S. texanus, one from Europe and the other from California. An Illinois accession that has been published as S. texanus resolves here with S. donnellii. The Illinois material lacks spores and is thus difficult to identify morphologically, but is outwith the Southeastern Coastal Plain area where S. donnellii is thought to occur.

The next steps in this study involve a second pass through the DNA extractions, to see if using other PCR additives will help increase the sequence success rate, then combining the sequence data from the three sequenced loci into a single matrix, to produce a more robust and supported phylogeny. Description of new species, where required, will fall under Daniela’s remit, in line with the comprehensive taxonomic revision that she has carried out.

 

Links & References:

Sphaerocarpos, preview to a monograph

BFNA | Family List | BFNA Vol. 3 | Sphaerocarpaceae

BBS Field Guide Sphaerocarpos michelii / texanus

Sep 122016
 
Photo 11-09-2016, 12 14 22

The tiny liverwort Colura calyptrifolia (photographed with an iPhone and a x20 handlens!)

Colura calyptrifolia (or to give it its appropriately creepy-sounding common name, the Fingered Cowlwort), is one of our most fascinating UK liverworts. Absolutely tiny (the leaves are about a millimetre long and whole plants often only 2-3 mm), it is heavily modified from the basic leafy-liverwort body plan, the leaves formed into inflated sacs like miniscule balloons with pointed “beaks” at one end. These tiny sacs have even tinier trapdoor-like flaps that only open inwards, allowing them to capture ciliate protozoa and other microscopic creatures (conclusively observed in another species of the same genus). It’s not yet certain if the liverwort gains nutrients from “swallowing” these animals, although this might be a reasonable hypothesis given the similarity of the mechanism to that found in much larger carnivorous plants such as bladderworts.

Photo 11-09-2016, 12 14 20

The leaves of Colura are modified into tiny ballon-like sacs that trap small animals

This colony was spotted yesterday in Anglezarke, Lancashire following the British Bryological Society (BBS) AGM in Manchester. Populations of Colura have undergone a spectacular expansion over the last 10 or 20 years, particularly in conifer plantations where they occur as tiny epiphytes. Previously the plant was rather rare, occurring mostly on rock in humid gullies and restricted to the wetter areas of the far west. This sighting was on the trunk of a willow at the edge of a reservoir.

Something else that has changed rapidly over the last 10 or 20 years is the ease with which small things can be photographed and shared. These pictures were taken simply by pointing the camera of an iPhone through a x20 handlens (the latter much cheaper than an iPhone and even more useful!),  and if we had wished could have been made available online instantaneously. As poorly-known biodiversity is increasingly threatened globally, should we be making better use of cheap imaging and real-time networking of expertise to facilitate species discovery and monitoring?

 

References

Barthlott, W., Fischer, E., Frahm, J.-P. & Seine, R. (2000). First Experimental Evidence for Zoophagy in the Hepatic Colura. Plant Biology 2(1):93-97. 

Blockeel, T L, Bosanquet, S D S, Hill, M O and Preston, C D (2014). Atlas of British & Irish Bryophytes. Pisces Publications, Newbury.

Sep 082016
 

One of the main problems with sampling largely from herbarium specimens, rather than from material that has been specifically collected for DNA work (rapidly dried in silica gel then maintained at low humidity), is that the quality of the DNA is unpredictable and usually rather poor. Therefore, despite starting out with 169 accessions and about 20 species of Marchantia, the actual successes, where we were able to get good quality DNA sequence data, were substantially lower. What we currently have is a slightly unbalanced data matrix, with 82 Marchantia accessions for rbcL, and 78 Marchantia accessions for psbA-trnH.

Reboulia hemisphaerica thallus, photographed by David Long (Long 34254)

Reboulia hemisphaerica thallus, photographed by David Long (Long 34254)

We also sequenced both rbcL and psbA-trnH from material of two accessions that we thought were Marchantia but where the sequences turned out to be Reboulia (from Texas) and Wiesnerella (from Bhutan). A quick check of the herbarium voucher specimens for both of these showed that they represented mixed collections of more than one complex thalloid species, for which the “wrong” plant parts had ended up in our silica dried tissue collection. Taking fortune from misfortune, both Reboulia and Wiesnerella form quite adequate outgroups for the phylogeny!

Wiesnerella denuda, photographed by David Long

Wiesnerella denuda thallus, photographed by David Long (Long 36267)

Out of the 20 species that we HAD hoped to sample, we ended up with only 12 named Marchantia species for rbcL (Marchantia polymorpha, M. paleacea, M. linearis, M. papillata, M. inflexa, M. emarginata, M. pinna, M. chenopoda, M. debilis, M. hartlessiana, M. quadrata and M. romanica), and 15 for psbA-trnH (Marchantia polymorpha, M. paleacea, M. linearis, M. papillata, M. inflexa, M. emarginata, M. pinna, M. chenopoda, M. debilis, M. globosa, M. pappeana, M. hartlessiana, M. subintegra, M. quadrata and M. romanica); we also had three Marchantia polymorpha subspecies (polymorpha, ruderalis and montivagans) and two Marchantia paleacea subspecies (paleacea and diptera).

That’s a little disappointing, representing, as it does, fewer than half of the 38 currently recognised species in the genus. However, we did also sequence a number of Marchantia accessions that had not been determined to species, and although many of them were good DNA matches to species that we had sampled, several are clearly different to everything else that we have included: one distinct lineage in Yunnan, China, another that occurs in Yunnan and Nepal, and a third in Indonesia and Malaysia. That’s balanced again by taxa that may not have been identified correctly; the psbA-trnH sequences from African material of M. debilis, M. globosa, M. pappeana and M. polymorpha, for example, are identical.

Intriguingly, in the “Preissia” clade, as well as M. romanica, there appear to be two lineages of Marchantia quadrata, one consisting of accessions from Denmark, Sweden and Sichuan, China, and the other with accessions from Svalbard, Norway and Utah, USA. These may tie in with subspecies quadrata (for the first lineage) and subspecies hyperborea (for the material from Svalbard and Utah), but the degree of genetic divergence is far higher than that found between many of the recognised species in Marchantia. It is a bit disconcerting, however, to notice that we have managed to overlook any Marchantia quadrata material from Scotland in our sampling!

The next step in the project, before it’s time to reveal any of the phylogenetic trees I’ve alluded to, is a phase of reciprocal illumination where we reconcile morphological information from the herbarium specimens with the information derived from the molecular sequence data. In other words, it’s time to double check our plant identifications, a part of the project that’s now in the capable hands of Dr David Long; the pile of Marchantia specimens is already on his desk!

 

 

Relevant posts

A rapid phylogeny of Marchantia, from the RBGE collections. I. Sampling

A rapid phylogeny of Marchantia, from the RBGE collections. II. Illuminating our sampling

Aug 122016
 

University of Edinburgh/RBGE student Lucy Reed, studying for the Masters degree in the Biodiversity and Taxonomy of Plants; thesis submitted August 2011.

Supervisors: Dr David Long, Dr Michelle Hart and David Bell.

The leafy liverwort genus Plagiochila is known for high levels of infraspecific morphological variation and blurred species boundaries. To address this, Lucy sequenced the plastid rbcL and matK plant barcode loci, along with the plastid psbA-trnH spacer, and the nuclear ITS region, assessing the genetic distinctiveness of four British taxa of Plagiochila sect. Plagiochila (Plagiochilaceae), as part of our wider project to DNA barcode the British bryophyte flora. The molecular matrix consisted of sequences from 14 accessions of P. asplenioides, 15 accessions of P. britannica, 3 accessions of P. norvegica, 7 accessions of P. porelloides, and two accessions that were not confidently identified to any species. Most of the samples came from across the UK, although plants from Ireland, Italy, Norway, Sweden and Switzerland were also included. Several outgroups were also available – 5 accessions of P. carringtonii, 3 accessions of P. heterophylla, 3 accessions of P. bifaria, 4 accessions of P. punctata, 5 accessions of P. spinulosa, and 2 accessions of P. exigua.

Lucy also undertook a herbarium study, to revise morphological characters for the taxa and correlate them with the molecular results. She scored a range of non-reproductive characters, using 13 of these for Principal Component Analysis (PCA). Because the plants are dioicous, using reproductive characters would have required male and female plants; furthermore, sporophytes are rarely collected, and not known at all for P. norvegica.

Using the three plastid markers rbcL, matK and psbA-trnH, Lucy resolved two species groups – a P. asplenioides-P. brittanica group, and a P. porelloides-P. norvegica group. The branch lengths for tree produced from the regions that she sequenced were, however, short and statistical support was absent, so the markers could not reliably be used to distinguish P. asplenioides from P. britannica, or P. porelloides from P. norvegica. On the other hand, only one of the 7 P. britannica accessions that was successfully sequenced for ITS resolved with P. asplenioides; the rest resolved with P. porelloides. Again, branch lengths within clades were too short to confidently distinguish species.

Species summaries:

  1. Plagiochila asplenioides: Lucy considered this species to be relatively easy to distinguish, because of its larger and more robust habit and larger leaves. There was, however, potential for confusion when dealing with smaller plants. However, in combination with DNA sequence data from the four loci, most individuals could be identified.
  2. Plagiochila porelloides: Lucy found that molecular sequence data could clearly separate this species from P. asplenioides and P. britannica. However, P. norvegica, which is separated from P. porelloides mainly by leaf apex shape and leaf margin tooth size, was not distinguishable using molecular data, and may be better either sunk, or reduced to a variety of P. porelloides, which already contains a lot of morphological variability.
  3. Plagiochila britannica: Lucy proposed that discrepancies between the plastid and nuclear gene topologies could be down to a hybrid origin for this species, fitting the diploid (n=18) status of the plant, as opposed to the haploid (n=9) status of both P. asplenioides and P. porelloides (key references: Paton, 1979; Newton, 1986).
  4. Plagiochila norvegica: originally described from Norway, this species has subsequently been found in Sweden and in England. Lucy included samples from England and Norway, but found no molecular evidence that they were distinct from P. porelloides, while the morphological differences that separate the taxa could be related to environmental conditions (Paton 1999).
Plagiochila asplenioides vice county 79 Long 8476

Plagiochila asplenioides vice county 79, Long 8476; photographed by David Long

Plagiochila britannica vice county 50, Long 37707

Plagiochila britannica vice county 50, Long 37707; photographed by David Long

 

Related Posts

Student projects at RBGE: DNA barcoding British liverworts: Lophocolea

Student projects at RBGE: Barcoding British Liverworts: Plagiochila (Dumort.) Dumort.

Student projects at RBGE: Barcoding British Liverworts: Metzgeria

Student projects at RBGE: DNA barcoding of the leafy liverwort genus Herbertus Gray in Europe and a review of the taxonomic status of Herbertus borealis Crundw.

Jul 192016
 
Decaying wooden fence, between concrete poles, Kufstein, Austria

Decaying wooden fence, between concrete poles, Kufstein, Austria

Recently in Kufstein, the home of Austrian bryologist Wolfgang Hofbauer, the demolition of an attractive old building and clearing of trees and other plants from the land, leaving a bare gravel patch used as a parking space, did have one interesting outcome: The new clearing led Wolfgang’s eye to a decaying wooden fence between concrete posts. Both the posts and the fence are partly covered in bryophytes, but among them, Wolfgang was very surprised to find the moss Schistidium growing on the old wood as well as on the concrete.

Schistidium on fence post, Austria

Schistidium on fence post, AustriaIn the bryological literature, the only reference to the plant growing on wood is a rare occurrence of Schistidium apocarpum, on lime-impregnated tree bark. The situation in this Kufstein parking lot seems unique, with at least two different species of Schistidium on the wood (although species identification is ongoing). Other more typical residents of old wood, which are also present, include Leucodon sciuroides, Orthotrichum affine and Hypnum cupressiforme. However, the unique assemblage is unlikely to last, as the climatic regime at the place will have changed following the removal of the trees, and the newly exposed rotten fence will probably soon be replaced.

Schistidium on fence post, Austria

Schistidium on fence post, Austria

Meanwhile, however, we wonder if similar unlikely assemblages of mosses are being observed elsewhere, and if there is an explanation for any potential changes in habitat?

 

 

Botanics Story and images provided by Wolfgang Hofbauer

 

Related literature

Wolfgang Karl Hofbauer, Laura Lowe Forrest, Peter M. Hollingsworth, Michelle L. Hart. 2016. Preliminary insights from DNA barcoding into the diversity of mosses colonising modern building surfaces. Bryophyte Diversity and Evolution 38(1).

Sam Bosanquet. 2010. Schistidium species reports, in: Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society.

In plain sight – the mosses that grow on British walls. http://stories.rbge.org.uk/archives/19957

Hidden diversity in unexpected places – moss growth on modern building surfaces. http://stories.rbge.org.uk/archives/17489

 

May 132016
 

Plant diversity does not have to be far-flung and exotic to be worth studying; even within Scotland, there are unanswered questions about plant distributions. Growing in our towns and cities, sharing our walls and pavements, there are bryophytes, tiny mosses and liverworts. We pass these every day, step over them, walk past them, hardly noticing that they are there. Miniature ecosystems form in the mosses that grow in the mortar between our bricks, or cling to cement surfaces of our bridges, and yet, partly because they are so commonplace, we don’t usually see them at all. And we have amazingly little understanding of exactly which species are involved, or where they have come from.

Recently, we looked at plants of the common moss Schistidium to find out exactly which species grow on artificial surfaces, like cement, walls and roofs (Hofbauer et al. 2016). Our study included plants from different geographic areas, with many plants collected in Germany and Austria, where Wolfgang Hofbauer, the lead researcher on the study, works and lives. However, a small subset of the plants were collected in the UK, and so also form part of the Royal Botanic Garden Edinburgh’s “Barcoding the British Bryophytes” project. Of 29 Schistidium plants collected in the UK, nine were collected on natural surfaces, like boulders and cliffs, and 17 were collected on artificial surfaces, like walls and roofs (for three accessions we don’t have a record of what kind of surface they were growing on).

Schistidium, photographed by Wolfgang Hofbauer

Schistidium, photographed by Wolfgang Hofbauer

These UK moss samples probably belong to eight species, Schistidium crassipilum, Schistidium pruinosum, Schistidium elegantulum, Schistidium strictum, Schistidium papillosum, Schistidium apocarpum, Schistidium trichodon and Schistidium dupretii, with three of the species, Schistidium crassipilum, Schistidium elegantulum and Schistidium apocarpum, having been collected from both natural and man-made surfaces.

A diagram of genetic relationships between the plants we sampled is shown below.

Schistidium crassipilum – we found three distinct genetic types within this species, which may belong to different species or subspecies. Schistidium crassipilum is known to be common on man-made habitats across Britain and Ireland, and we have collected it on bricks, cement, and even roofs as well as on natural substrates.

Schistidium pruinosum – only one of the moss plants in the study, collected in the Pentlands near Edinburgh, belonged to this species. It’s not known from many collections in the UK, although this may just be because the plants are often overlooked or misidentified, rather than that they are rare.

Schistidium elegantulum – this has been reported from natural and man-made habitats to the south and west of Britain. However, in our study, we have found it growing in the east, on cement in East Lothian and Midlothian, as well as in some more traditionally westerly locations in Scotland.

Schistidium papillosum – only one of the moss plants in this study, collected from limestone in Craig Leek, near Braemar, probably belongs to this species.

Schistidium strictum – again, only one of the plants in our study, collected in Dumfries on rocks, probably belongs to this species.

Schistidium papillosum is sometimes considered to be the same species as S. strictum (e.g. by AJE Smith 1978, The Moss Flora of Britain and Ireland, Cambridge University Press, but not by Bosanquet 2010, p. 515, in Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society), although we did find genetic differences between the two plants that we sampled, consistent with their recognition as two separate species.

Schistidium apocarpum – this is one of the more common Schistidium species, and known to occur on natural and man-made surfaces; we sampled several plants from this species, growing on walls and rocks.

Schistidium trichodon – described as “a rare upland calcicole” by Sam Bosanquet (2010, p. 515, in Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society), both our collections matched the reported habitat, growing on limestone, in Clova and Feith, Scotland.

Schistidium dupretii – we only sampled a single British accession of this species, another rare calcicole, which had been collected at Ben Lawers.

We are still far from having full records of how much genetic diversity there is in Schistidium in the British Isles. Partly because our previous work has focused on mosses on man-made surfaces, we don’t yet have any data for several other species that have been reported from Britain and Ireland (Bosanquet 2010, in Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society). These include Schistidium maritimum (reportedly usually northern and western, in coastal locations), Schistidium rivulare (commonly around water, particularly fast-flowing rivers), Schistidium platyphyllum (another species that grows near rivers), Schistidium agassizii (rare, aquatic and probably often overlooked), Schistidium flexipile (very infrequent, with only one record from recent years), Schistidium robustum (an uncommon upland calcicole), Schistidium confertum (an uncommon upland species), Schistidium frigidum (yet another uncommon reportedly upland species) and Schistidium atrofuscum (a rare moss, only recorded for the UK in the central Highland area).

But at least we are now starting to get a better picture of the mosses that share our towns and cities!

 

UK Schistidium accessions, parsimony analysis of ITS data with bootstrap support above branches

UK Schistidium accessions: parsimony analysis of nuclear ITS DNA sequence data, with bootstrap support above branches

 

Acknowledgments
This work was supported by EU SYNTHESYS project (http://www.synthesys.info) gb-taf-3881.
Thanks are also due to David Long for providing many of the specimens.
.
.
References

Wolfgang Karl Hofbauer, Laura Lowe Forrest, Peter M. Hollingsworth, Michelle L. Hart. 2016. Preliminary insights from DNA barcoding into the diversity of mosses colonising modern building surfaces. Bryophyte Diversity and Evolution 38(1)

Sam Bosanquet. 2010. Schistidium species reports, in: Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society.

Apr 262016
 
Setting up PCRs in our laminar flow hood

Setting up Aneura PCRs in our laminar flow hood

Sitting in Edinburgh airport on a Monday morning, waiting for David Long to join me, checked in through to Trondheim via Copenhagen, I felt completely unprepared. The previous week had been a fluster of lab work and reading DNA sequences, trying to get everything ready in time – a stressful Friday evening, trying to copy all the Aneura files into my Dropbox and onto flash drives before the building shut down at 6pm, willing all the file transfers to go faster and faster… but in the end having to leave many of the images that I had planned to take with me behind in the office. Despite a relatively early start on the Monday, we had a 7 hour layover in Copenhagen,

The Lego shop, Copenhagen

The Lego shop, Copenhagen

time for a train ride into the city, lunch, and a meander through the downtown streets, so didn’t get to Trondheim until late. From the airport bus we could make out snow and birch trees, before getting off on a near-deserted icy street. A short walk to the Comfort Hotel Park, an easy check-in, and sleep.

Swedish bryologist Lars Söderström picked us up in the foyer at about 9am. The university is only 20 minutes or so walk away, but the icy pavements made that impractical, so we were taking the bus. Lars had our bus tickets on his phone, cheaper and easier than using cash on the bus. Once purchased, they’re good for an hour and a half, with a spinning bar that gets shorter over the time period until it eventually disappears and the ticket has gone. It was a short ride, across the river and uphill, through mostly painted wooden buildings. Ana Séneca, our Portugese team-Aneura colleague, met us on the bus.

The university building is modern and airy, with open atriums the height of the building, planted with dead bamboo. Ana and I made our way to the Herbarium, a windowless room filled with cupboards of bryophytes that had mostly been collected by herself and by Lars. This was the day that the two of us had put aside for compiling and analysing our Aneura data. I’d begun sending sequences over to Ana on the Friday, so the datasets were already joined together. We had sequences from just over 300 accessions of Aneura, mostly from the British Isles and Norway, but with representatives from Albania, Sweden, Iceland, Portugal, Belgium, Austria, Latvia, the Faroe Islands, China, Fiji, India, the Falklands, Reunion, South Africa, the US, Canada, Panama, Peru…

Building phylogenetic trees in the University Herbarium, Trondheim

Building phylogenetic trees for Aneura in the University Herbarium, Trondheim

We used PAUP to run some quick parsimony analyses, printing out multi-page phylogenetic trees for each of four gene regions that we had been sequencing.

Papering over the table with our Aneura data

Papering over the table with our Aneura data

Clades that were in common between all four trees were marked on using some provisional, and informal, clade names, and after a search for coloured crayons, Ana undertook the serious business of marking geography onto the trees. Although she tracked down a pack of 12 coloured crayons, that wasn’t quite enough to separate the regions we were interested in, so we ended up with a key that combined colour and symbols.

Back to basics - colouring in the trees

Back to basics – colouring in the trees

A little after 5pm, it was time to call it a day, roll up the trees we’d made, and head out into the cold and dark to catch the bus back into town; the four of us headed to the Microbrewery in town for beer and burgers, then a nightcap of whisky at the hotel before Lars and Ana caught the bus out to their home.

Lars, David and Ana pick their way across the least icy route to the Museum

Lars, David and Ana pick their way across the least icy route to the Museum

The next morning, Lars and Ana met us at the hotel again, but this time instead of a bus, we were walking to the Museum, only five minutes or so from where we were staying. The paths were icy, but the views across the river were beautiful in the sunlight. We signed in at the Museum, where our Norwegian friend and colleague, Kristian Hassel, was waiting. First we headed up to the Herbarium, with views out across the city, before going downstairs for coffee, and settling on a sofa in the library to roll out our trees and start the conversation – what are we going to do with this data?

View from the Herbarium, NTNU Museum

View from the Herbarium, NTNU Museum

Luckily, we all agreed on the next actions – we are going to give names to a set of new species, based on molecular characters. We won’t name things that have only been collected and sequenced once, but if there are 4 or more accessions that form a lineage, then they will get named. Because of the focus of our sampling, we will restrict the taxonomy to taxa that occur in Europe. We also have to deal with the species of Aneura that have already been described. Because we are planning to use DNA for taxonomy, then we need to also have sequence data for all the existing names in the genus, even those that were described before anyone know what DNA was. This can be done retrospectively, using epitypification.

Ana and Lars compare names in the Museum library

Ana and Lars compare names in the Museum library

When a species name is published, it is linked to something known as a ‘type’. Usually this is a physical specimen, botanically, a dried out plant sample, although historically, illustrations were also used. The specimens are particularly important, often placed in special red folders, and treated with great respect. Methods like DNA extraction, which involve physically destroying parts of the material, are frowned upon. Given that some of the material can be over a hundred years old, DNA methods can also have very low success.

Instead of trying to get hold of old plant types and grind them up, we intend to use an alternative, which is the designation of new good-quality plant material as ‘epitypes’ – explanatory types that have more characteristics than the original material had, and so allow a better understanding of the correct application of the plant name. The material that we will designate as epitypes will be from large collections, with associated DNA material, and will have been sequenced for the set of four DNA markers in our project.

Trondheim, by the river

Trondheim

Trondheim

Trondheim

Thursday saw us back in the University, continuing discussions about data handling, dealing with mundane tasks like tracking down specimen information and compiling tables of data. More excitingly, bringing together collection details for plants in different evolutionary groups in our trees started to reveal some biology behind our proposed new species, with different ones occurring in different habitats. Although our departure on the Friday morning can only be described as totally uncivilised, with a 6.30 am flight from Trondheim to Oslo, a short stopover then an arrival in Edinburgh at approximately breakfast time, at least we had the satisfaction that the story of Aneura is finally beginning to come together – and an agreement that the next time we meet, it will be somewhere a bit less frozen, like Portugal…

A land of snow and ice - Norway from the plane

A land of snow and ice – Norway from the plane