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

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 092016
 
Sphaeropcaros texanus photographed by David Long (Long 33162)

European material of Sphaerocarpos texanus, photographed by David Long (Long 33162)

The Sphaerocarpales (or “Bottle Liverworts”) form a very distinct group in the complex thalloid liverworts, with ca. 30 species in five genera: originally the group just included Geothallus (monospecific), Sphaerocarpos (8-9 species) and Riella (ca. 20 species), with two more monospecific genera, Austroriella and Monocarpus, added within the last few years. All five genera have very unusual, and highly reduced, thallus morphologies. With the exception of Monocarpus, they also all enclose their sex organs (or gametangia – the antheridia and archegonia) in inflated flask-shaped bottles (as can be seen in the accompanying photograph). This feature sets them apart from all other liverworts. All of them are adapted to extreme habitats, including arable fields, hot arid regions, seasonal lakes and pools, and salt pans.

A worldwide revision of the second largest genus of the group, Sphaerocarpos, is over 100 years old (Haynes 1910); other revisional work focuses on individual geographic areas, including South Africa (Proskauer 1955), North America (Haynes & Howe 1923, Frye & Clark 1937, Schuster 1992, Timme 2003), California (Howe 1899), Europe (Reimers 1936, Müller 1954), and France (Douin 1907). No revisions have been made for large areas including Australia, Asia and South America, and most of the work predates any DNA-based concepts of plant identification or species relationships. Bringing the taxonomy of Sphaerocarpos into the 21st century, Dr Daniela Schill spent 18 months (2007-2009) at RBGE on a Sibbald Trust-funded project to compile a world-wide taxonomic revision of the genus. Two field expeditions fed into the project, with Dr David Long collecting European species in Portugal in April 2007, and Daniela collecting North American species in California in March 2008 (funded by the Peter Davis Expedition Fund).

Spore SEMs of Sphaerocarpus drewiae, taken by Daniela Schill

Spore tetrads of Sphaerocarpos drewiae, SEMs taken by, and plate prepared by, Daniela Schill

Daniela’s work is based on morphological and anatomical characters, including spore characters that she observed using Scanning Electron Microscopy (SEM). Her aim has been to produce identification keys to the species, species descriptions, species lists, synonyms, botanical drawings, distribution maps, and ecological, nomenclatural and taxonomical notes. Although the study is not yet published, much of it, including SEM plates for spores from the ca. 9 different species (as seen on the right), is complete.

In parallel, RBGE staff have also been sequencing multiple accessions of all available Sphaerocarpos species, producing data that has helped inform some of Daniela’s taxonomic decisions, and that also allow us to generate a stand-alone phylogeny for the genus.

This research will lead to some taxonomic changes. For example, European Sphaerocarpos texanus plants differ from American S. texanus, both in their DNA sequences and in their spore characters, and so they are likely to be considered a separate species. Furthermore, European Sphaerocarpos michelii material includes three different forms based on spore characters; these are also confirmed by molecular research, and may be recognised at or below the rank of species.

 

References:

Cargill, D.C. & J. Milne. 2013. A new terrestrial genus and species within the aquatic liverwort family Riellaceae (Sphaerocarpales) from Australia. Polish Botanical Journal 58(1): 71-80.

Douin R. 1907. Les Sphaerocarpus français. Revue Bryologique 34(6): 105-112.

Frye T.C. & L. Clark. 1937. Hepaticae of North America. University of Washington Publications in Biology 6: 105-113.

Haynes C.C. 1910. Sphaerocarpos hians sp. nov., with a revision of the genus and illustrations of the species. Bulletin of the Torrey Botanical Club 37(5): 215-230.

Haynes C.C. & M.A. Howe. 1923. Sphaerocarpales. North American Flora 14: 1-8.

Howe  M.A. 1899. The hepaticae and anthocerotes of California. Memoirs of the Torrey Botanical Club 7: 64-70.

Müller K. 1954. Die Lebermoose Europas. In: Rabenhorst’s Kryptogamenflora von Deutschland, Österreich und der Schweiz. 3. Auflage. Volume VI. Part 1. Leipzig, Akademische Verlagsgesellschaft Geest & Portig K.-G., Johnson Reprint Corporation (1971), New York, London.

Proskauer J. 1955. The Sphaerocarpales of South Africa. The Journal of South African Botany 21: 63-75.

Reimers H. 1936. Revision des europäischen Sphaerocarpus-Materials im Berliner Herbar. Hedwigia 76: 153-164.

Schill D.B., L. Miserere & D.G.Long. 2009. Typification of Sphaerocarpos michelii Bellardi, S. terrestris Sm. and Targionia sphaerocarpos Dicks. (Marchantiophyta, Sphaerocarpaceae). Taxon 58(2): 638-640.

Schuster R.M. 1992. Sphaerocarpales. In: The hepaticae and anthocerotae of North America V. Field Museum of Natural History, Chicago: 799-827.

Timme S.L. 2003. Sphaerocarpaceae. In: Bryophyte Flora of North America, Provisional Publication.

 

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

Sep 062016
 

University of Edinburgh/RBGE student David Bell, studying for the Masters degree in the Biodiversity and Taxonomy of Plants; thesis submitted August 2009.

Supervisors: Dr David Long and Dr Michelle Hart.

 

David used plastid DNA barcode markers rbcL (from 34 accessions) and psbA-trnH (from 36 accessions) to look at the four species of Herbertus in Europe, H. aduncus subsp hutchinsiae (British Isles, Norway and Faroes), H. stramineus (British Isles, Norway and Faroes), H. borealis (Scotland and Norway) and H. sendtneri (European Alps).

In addition to the four recognised taxa, David’s study identified a fifth species, later named as H. norenus, that occurs in Norway and the Shetland Isles.

A paper based on David’s MSc thesis work was published in Molecular Ecology Resources in 2012.

Herbertus norenus, photographed by David Long

Mixed sward including Herbertus norenus, photographed in Shetland by David Long

 

Bell et al. 2012, MER

 

 

Other student projects at the Gardens:

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

Aug 302016
 
EDNA label printer

The EDNA label printer in the office

Over the years, many different people have used the molecular laboratories at RBGE, to work on a multitude of projects on a multitude of plants and fungi. Some are staff members who stay for decades, others students who are only in the lab for a matter of months. Every time DNA is extracted and used in a molecular project, the amplified gene regions are processed and then the plastic tubes that they were in are sent for recycling – but the extracted DNA is kept in a DNA bank, in case it is needed for further research. Logistically, managing this DNA can be problematic. Scientists like to use their own numbering systems when they’re working (mine used to be one of the commonest – my initials followed by consecutive numbers, a system which worked perfectly until some of my extractions ended up in the same freezer as extractions by Dr Linda Fuselier), something quick and easy to scrawl onto the plastic tubes. This can link to collection information written in a lab-book, including who collected the plant, what date it was collected, and what country it came from. However, as people move on, and as the years pass, it becomes increasingly difficult to find any particular sample or set of samples, particularly when several sets of people share the same initials – and this is compounded by having to rummage through boxes of frozen DNA samples being kept at either -20° or -80°C. Few places at the Botanics are less pleasant than the dank room that contains our -80°C freezers!

 

Printed labels and EDNA tubes, Lab 32

Printed labels getting stuck onto EDNA tubes, Lab 32

The frustrations associated with rooting through inconsistently labelled DNA collections led Dr Michelle Hart and Alex Clarke, in 2006, to instigate a standardised format for DNA labelling, with samples of DNA identified as part of the RBGE DNA bank and assigned EDNA numbers, the format of which consists of the year the DNA was banked, followed by a multi-digit identification number. For example, the last EDNA number that we have issued is EDNA16-0045851, for DNA extracted from the moss Weissia controversia. Due to uncertainties about institutional databases, in its early years the DNA bank was curated through Excel spreadsheets; this was revamped and upgraded in 2011 to the database that we still use today. Information about the methods and date of DNA extraction, the material’s collector, and the place of collection are all stored and easily retrieved, critical information if the DNA is going to be used to provide data for future publications. The EDNA number stays on all downstream files that are created from the DNA – lab books, raw sequence files, and it is also included as the isolate number in GenBank submissions – meaning that all molecular data generated at RBGE is still valuable after people have moved on and lab books have been mislaid.

 

EDNA tube

A labelled EDNA tube ready for the DNA sample, Lab 32

As to what happens to the actual DNA extraction, long-term storage involves transferring the liquid into a small barcoded and labelled tube in a lockable and numbered 96-tube rack, which will be kept on a labelled shelf in a -80°C freezer. The system is not perfect, however – banking or recovering the DNA samples still involves a trip to our mildewy bank room…

 

Pipelling DNA samples into EDNA tubes, Lab 31

Pipelling DNA samples into labelled EDNA tubes, Lab 31

Aug 122016
 

University of Edinburgh/RBGE student Kimberley Fackler, studying for the Masters degree in the Biodiversity and Taxonomy of Plants; thesis submitted August 2013.

Supervisors: David Bell, Dr David Long and Dr Laura Forrest.

 

Kim sampled from the six species of Metzgeria generally recognised to occur in the UK. She used standard DNA barcode markers rbcL, matK, psbA-trnH and ITS2.

Metzgeria furcata, vice county 49, Long 8069; photographed by David Long

Metzgeria furcata, vice county 49, Long 8069; photographed by David Long

Metzgeria furcata (L.) Dumort.

M. violaceae (Ach.) Dumort.

M. conjugata Lindb.

M. consanguinea Schiffn.

M. pubescens (Schrank)

M. leptoneura Spruce

Phylogram generated from accessions of Metzgeria species found in the UK

Phylogram generated from accessions of Metzgeria species found in the UK

 

DNA barcoding for all regions but rbcL delimited seven genetic lineages of Metzgeria within the UK. There was a lower amount of sequence variation in rbcL, suggesting that it is suitable for use at a higher taxonomic level than this genus.

Six of the genetic entities correspond to the current species concepts in Metzgeria. Metzgeria furcata was split into two sister groups, in line with the findings of Fuselier et al. 2009; these two groups may correspond to variety ulvula and variety furcata.

Conservation implications: If lineages do not have names, they have no legal recognition, no protection, and we cannot gather information about their rarity or distributions.

 

 

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.

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.

Aug 122016
 

University of Edinburgh Biotechnology student Kenneth McKinlay’s 4th year honours project, 2013. Supervisors: Dr David Long, Dr Laura Forrest

David Long and Kenneth checking out the Lophocolea on a decaying log in the Scottish Borders

David Long and Kenneth check out Lophocolea on a decaying log in the Scottish Borders

Kenneth barcoded all six species of British Lophocolea, L. bidentata, L. bispinosa, L. brookwoodiana, L. fragrans, L. heterophylla and L. semiteres, attempting to get data from three plastid regions (rbcL, matK, psbA-trnH) and one nuclear region (ITS2). The data generated from the rbcL and psbA-trnH regions was effective in discriminating between all the species sampled; however useful data were not obtained from matK or ITS2.

Genetic markers:

1. rbcL: bidirectional sequence data was generated for 38 accessions.

2. matK: amplification was not successful with the primer sets used (LivF1A, LivR1A).

3. psbA-trnH: bidirectional sequence data was generated for 40 accessions.

4. ITS2: although PCR amplification was successful for 35 accessions, the low quality of many of the sequences generated, and the presence of clear heterozygous positions in sequence data from some accessions, made this data set problematic to analyse, so it was excluded from the study.

Lophocolea bispinosa vice county 98 Long 4725

Lophocolea bispinosa vice county 98, Long 4725; photographed by David Long

Lophocolea semiteres vice county 98, Long 0578

Lophocolea semiteres vice county 98, Long 0578; photographed by David Long

 

 

 

 

 

 

 

 

Species and trees:

Distance tree generated using rbcL barcode sequence data for UK Lophocolea accessions

Distance tree generated using rbcL barcode sequence data for Lophocolea accessions, rooted on Chiloscyphus

L. fragrans – all accessions were genetically uniform, forming a monophyletic group.

L. heterophylla – although there was a little genetic variation, again, accessions of this species formed a distinct clade for both rbcL and psbA-trnH.

L. semiteres & L. brookwoodiana – these formed a single clade. All the accessions of L. semiteres (including material from the UK and Belgium) were genetically uniform, while two different genotypes were observed for L. brookwoodiana. While L. semiteres is known to be an introduced species in the UK, it’s possible that the three different genotypes in this clade represent separate introductions.

L. bispinosa – species formed a single genetically uniform group; this nests within a L. bidentata grade.

L. bidentata – accessions of this widespread and common species formed a grade, with three genetically distinct groups. One of these groups may represent L. cuspidata, a species that was sunk into L. bidentata by Bates and Walby in 1991, due to a lack of consistently distinguishing morphological characters. The results of this study suggest that a recircumscription of L. bidentata, “probably the commonest leafy liverwort in the British Isles” (Hodgetts, 2010), is required.

 

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.

 

 

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.
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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.