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!

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.

 

Jul 202016
 

Not long ago, the only non-crop plant that the mainstream scientific community seemed to be aware of was the brassica Arabidopsis thaliana – easily cultivated, with a short generation time and small nuclear genome, it seemed the perfect plant model. The model moss Physcomitrella patens came along some years later, again with a short generation time and small genome and with easy protocols for cultivation, but with the addition of a haploid dominant lifecycle and the ability to undergo efficient homologous recombination. A far more recent addition to the pool of available model organisms is the complex thalloid liverwort Marchantia polymorpha. Like Physcomitrella, the haploid part of the plant’s lifecycle is dominant, the nuclear genome is small, the plants are easy to cultivate and fast growing, and there are established protocols to get them into sexual phases. Genetic transformation is also straightforward, and because the thalloid plant is haploid, the effects of mutations are easily visible and can be propagated via vegetative clones.

model system posterIndicative of its growing popularity as a model organism, the February 2016 edition of Plant and Cell Physiology, edited by Professors John Bowman, Takashi Araki and Takayuki Kohchi, was a special focus edition on Marchantia polymorpha, while in June this year, EMBO hosted an international workshop on new model systems for early land plant evolution, wherein 21 of 36 speakers (58%) and 43 of 67 poster presenters (64%) mentioned Marchantia in their abstracts.

Marchantia sampling from Villarreal et al. 2015

Marchantia species sampling from Villarreal et al. 2015, New Phytologist

With publications starting to emerge from the longstanding RBGE project on the phylogeny of complex thalloid liverworts, we felt it was time to also explore some of the species level variation within genera. Previous published work from RBGE examines species relationships in other complex thalloid groups, Dumortiera, Cleveaceae and Mannia, while we are currently working on manuscripts for Sphaerocarpos and for the Aytonicaeae.

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

Some of the collections of Marchantia held in the RBGE herbarium

Boxes of silica-dried liverworts in RBGE's tissue storage room

Boxes of silica-dried liverworts in RBGE’s tissue storage room

Considering the current levels of interest in Marchantia, and in light of our recent paper sinking both Preissia and Bugecia into the genus, we did a rapid survey of our silica-dried tissue and herbarium collections, to see how feasible it was to flesh out the sampling in our 2015 paper (which included about 8 species), to produce the first phylogeny for species of Marchantia. In 2013-2014, we extracted DNA from all our silica-dried tissue collections, and from many of the most recent herbarium collections, which in combination with sampling for our complex thalloid phylogeny, various EU-funded SYNTHESYS projects, and ongoing DNA barcoding work, meant that we now have DNA extracted from 169 Marchantia accessions, which have been determined to represent ca. 20 species, out of a total of 38 accepted species in the genus.

Marchantia polymorpha ssp montivagans, photographed in Merida, Venezuela by David Long

Marchantia polymorpha ssp montivagans, photographed in Merida, Venezuela by David Long (Long 33064)

However, nearly 45% of the accessions (76) are detted as Marchantia polymorpha, as some of our previous work has focused on investigating the genetic differences between its three recognised subspecies, ruderalis (the common, weedy form), polymorpha (from damp natural habitats) and montivagans (frequently an upland plant). Most of the Marchantia polymorpha accessions are from the UK, but there are also samples from Ireland, Portugal, Sweden, Latvia, Switzerland, France, China, Malaysia, Pakistan, Tanzania, the US, Canada, Argentina, Ecuador and Peru.

The other species that we have extracted DNA for are M. alpestris, from Greenland; M. berteroana, from Chile and New Zealand; M. chenopoda, from Ecuador and Mexico; M. debilis from Cameroon, Ghana and South Africa; M. emarginata, from China and Japan; M. foliacea, from New Zealand; M. globosa, from Reunion; M. hartlessiana, from Bhutan, India and Nepal; M. inflexa, from Mexico; M. linearis, from Bhutan and Nepal; M. paleacea, from Italy, Portugal, the US, Mexico, Yemen, India, Bhutan, China and Japan; M. papillata from Bhutan, Bangladesh, Nepal, Rhodesia, Tanzania and Malawi; M. pappeana from Lesotho, Tanzania and Malawi; M. pinnata from Japan; M. plicata from Ecuador, and M. subintegra from Bhutan, India and Nepal.

Marchantia quadrata, photographed in the US by David Long (Long 35670)

Marchantia quadrata, photographed in the US by David Long (Long 35670)

In addition, we have accessions of Marchantia romanica (formerly Bucegia romanica) from Romania and Slovakia, and accessions of Marchantia quadrata (formerly Preissia quadrata), from the UK, Ireland, France, Germany, Sweden, Norway, the Czech Republic, China and the US.

The choice of which DNA regions would be best to work with was straightforward – given that many of our DNA extractions were from herbarium specimens, we were limited to short regions of sequence, and to regions that are present in multiple copies within the plant genome – effectively, plastid and nuclear ribosomal regions. When specimens are preserved for the herbarium, the quality of their DNA drops considerably compared to fresh material; eventually it can break into many short fragments. In order to make copies of regions of DNA using standard laboratory PCR methods, there has to be an unbroken piece of DNA to act as the template, and the shorter the region that’s being copied, and the more copies of it that are present in the genome, the more likely it is to work. Because we routinely sequence the two standard plant DNA barcode loci, from the plastid rbcL and matK genes, and two supplementary DNA barcode regions, the plastid psbA-trnH spacer region and the nuclear ribosomal spacer ITS2, these relatively short regions were obvious choices. However, we found two of these regions, matK and ITS2, consistently problematic to amplify and to sequence for Marchantia polymorpha, and so decided to focus on just the rbcL and psbA-trnH regions for this initial study.

 

References:

David G. Long. 2010. Marchantia polymorpha subsp. montivagans/polymorpha/ruderalis, in: Atherton, Bosanquet & Lawley, Mosses and Liverworts of Britain and Ireland a field guide, British Bryological Society.

David G. Long, Laura L. Forrest, Juan Carlos Villarreal & Barbara J. Crandall-Stotler. 2016. Taxonomic changes in Marchantiaceae, Corsiniaceae and Cleveaceae (Marchantiidae, Marchantiophyta). Phytotaxa 252 (1): 077-080.

Juan Carlos Villarreal, Barbara J. Crandall-Stotler, Michelle L. Hart, David G. Long & Laura L. Forrest. 2015. Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate. New Phytologist. 209: 1734–46, doi: 10.1111/nph.13716.

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

Jul 062016
 

tempor

Vienna - the view from my 7th floor hotel room

Vienna in June – as seen from my hotel room

A couple of weeks ago I spent a few days in Vienna, my first visit in 11 years, when I was last over for the 2005 XVII International Botanical Congress. The location was practical – the hotel neatly nestled underneath a main road overpass, but extremely convenient from the airport, only a short train ride, and only minutes’ walk to the workshop venue, the Gregor Mendel Institute, where three days of talks and poster sessions on model early land plants were taking place. Arriving on the Tuesday evening, there was time to catch up with evolutionary biologist Dr Jill Harrison, a friend since our grad student days at RBGE, who has just moved her research group to the University of Bristol. The rest of my evening was spent fiddling with my slides for the talk I was giving the next morning.model system poster

Lecture theatre, Gregor Mendel Institute, with stairway scatter cushions

Lecture theatre, Gregor Mendel Institute, with stairway scatter cushions

Having attended a range of workshops in the past, nothing had quite prepared me for the scale of this one – with around 120 people registered, the large lecture theatre was packed, attendees spilling out to sit on cushions down the stairwells. Workshop organizers Professors Liam Dolan and Fred Berger opened the meeting, followed by a dazzling romp through Arabidopsis genomics from Professor Magnus Nordborg.

imagesTo introduce the next talk, I need a slight digression: If you are interested in land plant evolution, chances are you will have a copy of Dr Paul Kenrick and Peter Crane‘s The Origin and Early Diversification of Land Plants A Cladistic Study somewhere around your workspace. It was published in 1997, and my paperback copy is dog-eared and water-stained, having crossed the Atlantic more than once, and been lugged around various parts of the world in backpacks. My bookmark is still my deposit slip for the book: I ordered it in January 1998 from James Thin booksellers on South Bridge, Edinburgh, which obviously didn’t think local demand would be sufficient to keep copies in stock. (The book is still available to buy; sadly the bookshop went into administration in 2002.)

More than 18 years after buying and reading his book, this was the first time I’d actually heard Paul Kenrick speak, and it definitely goes down as one of the highlights of the meeting for me.  Clear, well paced and interesting, Paul led the audience through a concept of plant models that is very different to Arabidopsis-Physcomitrella-Marchantia.

Cupbarods full of liverworts in the RBGE Herbarium

Cupboards full of liverworts in the RBGE Herbarium

My own talk was a meander through the complex thalloid liverworts. The aim was to highlight the RBGE’s outstanding collection of dead complex thalloid plants, both as herbarium specimens and as silica dried tissue collections, and in addition, to point out some of the amazing non-Marchantia diversity within the group.

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

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

If I were composing my talk again today, it would be with an appreciation of two key facts about the audience that had not actually occured to me before the meeting. The first is that the other participants have an astounding understanding of their model plants’ form and function, at a level that far exceeds mine. The second is that an amazing resource of dead plants is not actually all that valuable to the evo-devo community, who are largely interested in what genes are expressed (transcriptomes, from RNA) and in what happens to plant growth when you change things – both of these require living material. Unfortunately, at RBGE we have extremely few bryophytes in the living collections – in fact, only two of which I am aware. We do incidentally have some rather spectacular quantities of Marchantia, although these have largely sprung up unrequested in an untended flowerbed….

A vast expanse of Marchantia polymorpha volunteers at RBGE

A vast expanse of Marchantia polymorpha volunteers at RBGE

Boxes of silica-dried liverworts in RBGE's tissue storage room

Boxes of silica-dried liverworts in RBGE’s tissue storage room

As the conference programme and abstracts are available online, however, I won’t go into any more detail about the talks, breaks, posters etc., but pick out a few key impressions. Overwhelmingly, mine are of a vast enthusiasm for experiment-driven natural history. Working out what things do, by trying to turn them off, and comparing that to what happens if you turn them on even brighter… the inevitable question if someone doesn’t mention this: “But have you tried overexpressing it?” Twisted curled balls of plant tissue, proliferating organs, and just general weirdness, all tied in to stories of How the Plant Became. Presentations of beautifully arranged slides, with professional quality illustrations. Internationality at all levels. And approachability.

An evening walk in Vienna, where we failed to find any Marchantia growing

An early evening walk in Vienna, where we failed to find any Marchantia growing

Sadly, I missed the last day of the meeting entirely, as I had another event scheduled – the Morag Alexander School of Dance annual show in Musselburgh. The show itself isn’t exactly a Once In A Lifetime experience – this one was the 7th annual dance show I’ve been to, but it was my daughter’s first ballet performance (for a few brief moments) on pointe. It did, however, mean missing what looked like a really enjoyable day of talks; in the light of short conversations earlier with both Dr Sebastian Schornack and Duke PhD student Jessica Nelson, theirs were two I was particularly disappointed to miss.

I am very grateful to Fred Berger and Liam Dolan for the invitation to come along and experience something that was, for me, just a little outside my regular molecular phylogeneticist comfort zone, but all the more interesting for that; and to Martina Gsar – the organization throughout was flawless. For the Physcomitrella and Marchantia evo-devo communities I have a short message: our plants may be mostly dead, and good for morphology and DNA only, but we are very happy to work with you in any areas that our fields overlap, and will welcome any of you who chose to visit us. Within the EU, funding to visit and work with natural history collections is available through the SYNTHESYS Access programme.

 

 

Jun 302016
 

The genus Aitchisoniella contains a single species, A. himalayensis, which was described by Pakistani botanist Professor Shiv Ram Kashyap from plants that he collected in Mussoorie, Uttarakhand, India (1914). Subsequently (1929) he also found the species in Shimla and Kullu in Himachal Pradesh. Although reports of new locations followed (Kanwal, 1977, Pant et al., 1992, Bischler et al., 1994), near Nainital in Uttarakhand, the species was only known from the north-west Himalayas of India until 2010, when its range was extended by RBGE bryologist Dr David Long, on the ‘Kunming/Edinburgh Expedition to Sichuan’. David found Aitchisoniella at two localities in China, in Litang and Daocheng counties of south-west Sichuan Province.

Athalamia pinguis, Sichuan, photographed by David Long (Long # 40305)

Fig. 1. Athalamia pinguis in Sichuan, showing stalked sexual branches (carpocephala), photographed by David Long (Long # 40305)

Aitchisoniella looks quite different to other complex thalloid liverworts: it doesn’t have the stalked sexual branches (carpocephala) that are present in most complex thalloid species like Marchantia, or Athalamia (as can be seen in the photograph, Fig. 1). Instead, the female sex organs (archegonia), and therefore the sporophytes, grow on the lower (ventral) side of a short receptacle (as can be seen in the photograph, Fig. 2). The receptacle is part of the main thallus, with air chambers and air pores, and a groove on the underside of the thallus from which characteristicly complex-thalloid pegged rhizoids grow.

 Aitchisoniella himalayensis in Sichuan showing terminal sporophyte-bearing receptacles, from Long 39886

Fig. 2. Aitchisoniella himalayensis in Sichuan, showing terminal sporophyte-bearing receptacles, photographed by David Long (Long # 39886)

Originally, Aitchisoniella was thought to belong to the Exormothecaceae family of complex thalloid liverworts, along with Exormotheca and Stephensoniella. Earlier this year, we transferred all the plants in Exormothecaeae into another family, Corsiniaceae, where they joined Corsinia and Cronisia (Long et al. 2016a).

Complex thalloid phylogeny reconstructed by Villarreal, J.C., B.J. Crandall-Stotler, M.L. Hart, D.G. Long, L.L. Forrest. 2015. Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate. New Phytologist. DOI: 10.1111/nph.13716

Fig. 3. The phylogenetic position of Aitchisoniella, from the complex thalloid phylogeny reconstructed by Villarreal et al. (2015)

However, having fresh material of the plant meant that we were able to extract DNA from it, and add it into our molecular phylogeny for the group (Villarreal et al. 2015). The results were unexpected, with Aitchisoniella grouping with species from a different complex thalloid family, Cleveaceae (Fig. 3). The growth forms are quite different, as all the species in Cleveaceae have got stalked carpocephala. However, once we started to think more about the evolution of these plants, and look more objectively at differences and similarities, one thing struck us: the spores of Aitchisoniella (see Fig. 4) look more like the spores of plants in Cleveaceae (e.g. Athalamia, Fig. 5) than they do like spores of plants in Exormothecaceae (e.g. Fig. 6).

Spores of Aitchisoniella himalayensis. (A) Distal view; (B) proximal view; (C) lateral view; (D) detail of distal view. (A and C) from Long 39886. (B and D) from Long 40020. Scale bars: (A–C) = 5 μm, (D) = 2 μm.

Fig. 4. Spores of Aitchisoniella himalayensis from Long et al. 2016: (A) Distal view; (B) proximal view; (C) lateral view; (D) detail of distal view. (A & C) from Long 39886. (B & D) from Long 40020. Scale bars: (A–C) = 5 μm, (D) = 2 μm.

Athalamia hyalina spore images from M. P. Steinkamp and W. T. Doyle American Journal of Botany Vol. 68, No. 3 (Mar., 1981), pp. 395-401

Fig. 5. Spores of Athalamia hyalina (Cleveaceae) from Steinkamp & Doyle (1981): 1. distal view (x 1,100); 2. proximal view (x 1,100); 3. equatorial view (x 1,100); 4. close-up of pore (x 6,000); 5. distal face (x 3,000).

 

Exormotheca spores: E. bulbigena - A, distal view, B, proximal view. E. holstii - C, distal view, D, proximal view, E, distal view, F, proximal view. From Bornefeld et al., 1996.

Fig. 6. Spores of Exormotheca from Bornefeld et al. (1996): E. bulbigena – A, distal view, B, proximal view. E. holstii – C, distal view, D, proximal view, E, distal view, F, proximal view.

Characters like spore shape used to be considered to be quite neutral in bryophyte evolution, features that were not really acted on by natural selection. Following this theory, spore characters were thought to be indicative of true and ancient relationships, changing very little across huge amounts of time. We have since moved away from this view, with, for example, small changes in the shape and size of spores known to have drastic effects on their aerodynamics. However, within the complex thalloids, it does seem that characters like the presence or absence of carpocephalum branches are quite variable within families, while spore morphology can be indicative of deeper relationships.

As a result of this work, based on both molecular and morphological evidence, we have transferred the genus Aitchisoniella to the family Cleveaceae (Long et al. 2016b), where it joins the four genera accepted by Rubasinghe et al. (2011): Athalamia, Clevea, Peltolepis and Sauteria.

 

REFERENCES

Bischler, H., Boisselier-Dubayle, M.C. & Pant, G. 1994. On Aitchisoniella Kash. (Marchantiales). Cryptogamie. Bryologie-Lichénologie, 15: 103–10.

Borenfeld, T., O.H. Volk & R. Wolf. 1996. Exormotheca bulbigena sp. nov. (Hepaticae, Marchantiales) and its relation to E. holstii in southern Africa. Bothalia 26,2: 159–165.

Kanwal, H.S. 1977. Marchantiales of district Naini Tal (Kumaun Hills) U.P., India. Revue Bryologique et Lichénologique, 43: 327–38.

Kashyap, S.R. 1914. Morphological and biological notes on new and little known West-Himalayan Liverworts. I. New Phytologist, 13: 206–26. doi: 10.1111/j.1469-8137.1914.tb05751.x.

Kashyap, S.R. 1929. Liverworts of the Western Himalayas and the Panjab Plain. Part 1. Lahore: The University of the Panjab.

Long, D.G., L.L. Forrest, J.C. Villarreal & B.J. Crandall-Stotler. 2016a. Taxonomic changes in Marchantiaceae, Corsiniaceae and Cleveaceae (Marchantiidae, Marchantiophyta). Phytotaxa, 252: 77–80.

Long, D.G., L.L. Forrest, J.C. Villarreal & B.J. Crandall-Stotler. 2016b. The genus Aitchisoniella Kashyap (Marchantiopsida, Cleveaceae) new to China, and its taxonomic placement. Journal of Bryology.

Pant, G., S.D. Tewari & S. Joshi. 1992. An assessment of vanishing rare bryophytes in Kumaun Himalaya – thalloid liverworts. Bryological Times, 68/69: 8–10.

Rubasinghe, S.C.K., D.G. Long, R. Milne & L.L. Forrest. 2011. Realignment of the genera of Cleveaceae (Marchantiopsida, Marchantiidae). The Bryologist 114: 116-127. http://dx.doi.org/10.1639/0007-2745-114.1.116.

Steinkamp, M.P. & W.J. Doyle. 1981. Spore wall ultrastucture in the liverwort Athalamia hyalina. American Journal of Botany 68: 395-401.

 

Villarreal, J.C., B.J. Crandall-Stotler, M.L. Hart, D.G. Long & L.L. Forrest. 2015. Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate. New Phytologist. 209: 1734–46, doi: 10.1111/nph.13716.

 

Long, D.G., L.L. Forrest, J.C. Villarreal, B.J. Crandall-Stotler. 2016. The genus Aitchisoniella Kashyap (Marchantiopsida, Cleveaceae) new to China, and its taxonomic placement. Journal of Bryology.

Mar 172016
 

One of the most recognisable groups in the bryophytes, the complex thalloid liverwort genus Marchantia, has just become a bit larger. We have sunk Preissia and Bucegia into it, because in molecular phylogenies they are both phylogenetically nested within Marchantia (Villarreal et al. 2015). Although this only adds two species to the genus (Preissia quadrata and Bucegia romanica), taking the total number of species recognised from 36 to 38, it also broadens the range of plant morphologies that occurs in Marchantia.

Marchantia sampling from Villarreal et al. 2015

Maximum likelihood topology for Marchantia from Villarreal et al. 2015; * indicates bootstrap support of 100% and posterior probabilites of 1

Preissia quadrata (Scopoli) Nees returns to an earlier name, Marchantia quadrata Scopoli. This is the name under which it was first described, by Scopoli, in 1772. For Bucegia romanica Rad., first described by Radian (1903), a new combination has been made, Marchantia romanica (Rad.) Long, Crandall-Stotler, Forrest & Villarreal.

A new subgenus, Marchantia subg. Preissia, has been created for these species. A third species that was collected in China by David Long, and was included in the molecular phylogeny, has not yet been named, but will also belong to subgenus Preissia. Morphologically, the new species is most similar to Marchantia quadrata.

bucegia paperMarchantia romanica is known from northern Europe and northern North America (e.g. Evans 1917, Konstantinova et al. 2014). Photographs of fertile plants, and transverse sections showing 2-3 layers of filament-less air chambers, can be seen in Konstantinova et al.’s report. The hollow air chambers they illustrate are one of the clearest features that separated Bucegia from Marchantia and Preissia.

Preissia quadrata carpocephalum, photographed by Des Callaghan

Marchantia quadrata carpocephalum, photographed by Des Callaghan

Marchantia quadrata is also a northern hemisphere species; it is widespread in the British Isles, and a map and photographs are available in the British Bryological Society Field Guide. Like Marchantia romanica, this species lacks gemmae cups. Its two ranks of ventral scales could also be used to separate Preissia from Marchantia, which typically has 4 or more rows of ventral scales. Two subspecies are recognised in Schuster (1992), one more southerly and dioicous (ssp quadrata) and the other northern and monoecious (ssp hyperborea) (Schuster 1985). From our data, using DNA regions from genes that were chosen to show relationships between genera rather than within species, genetic differences can be seen between a collection from the South Ebudes off the west coast of Scotland, and one from Snowbird, Utah in the United States. Molecular sampling from across the range of Marchantia quadrata may reveal a complex of several species. Indeed, this was anticipated by Schuster (1992, p. 366), who described the range of morphological variation within the species as “astonishing”.

Konstantinova et al. 2014: phylogentic variation between accessions of Bucegia and Preissia

Konstantinova et al. 2014: phylogenetic variation between accessions of Bucegia and Preissia

Konstantinova et al. (2014) generated DNA sequences for the nuclear ITS region, and two plastid regions, trnL-F and trnG, for six accessions of Marchantia romanica (“Bucegia”, from Romania, Ukraine and Svalbard), and three accessions of Marchantia quadrata (“Pressia”, from Russia). Unfortunately the regions that they sequenced do not overlap with the sequencing in our study, so we cannot combine the datasets. However, they do rather intriguingly resolve two clades within Marchantia romanica (“Bucegia”), one from mainland Europe, and the other from Svalbard. Again, molecular sampling from across the range of this taxon could reveal several distinct lineages. Adding samples from North America seems a priority.

Thus, although we have only added two species to Marchantia, the number of species is likely to rise with additional molecular sampling, in line with a clearly necessary taxonomic revision of Marchantia subgenus Preissia.

 

David G. Long, Laura L. Forrest, Juan Carlos Villarreal & Barbara J Crandall-Stotler. 2016. Taxonomic changes in Marchantiaceae, Corsiniaceae and Cleveaceae (Marchantiidae, Marchantiophyta). Phytotaxa 252 (1): 077-080.

 

Long et al

 

Nov 042015
 

The complex thalloid liverwort Monocarpus sphaerocarpus has been found on two continents, Australia and Africa, separated by around 8,000 km of mostly ocean. The green plants themselves are not particularly easy to compare, as the plants are small and the material that we have to work with has been squashed down and dried to form crumbly herbarium specimens. However, there are differences between the morphological descriptions of plants growing in Australia (Carr 1956; Proskauer 1961) and South Africa (Perold 1999). The characteristics of the plant’s spores are rather easier to observe (using scanning electron microscopy); this shows that spores from collections from Australia and South Africa are quite distinct – although there are also differences between spores from plants from Western Australia and Victoria.

Monocarpus spores: a,d: Victoria, Australia, b,e: Western Australia, c,f: Cape Province, South Africa

From Forrest et al. Fig. 4: Scanning electron micrographs of Monocarpus spores: a,d: Victoria, Australia, b,e: Western Australia, c,f: Cape Province, South Africa.

Although the distances between the three regions in which Monocarpus has been found are huge, it is possible that populations of Monocarpus are more widespread than we might expect. Dust storms could lift spores into the atmosphere, and the dark coloration of the spores suggests some ultraviolet resistance. Proskauer (1961) was able to grow sporelings from four-year-old herbarium collections, showing that they can survive drying out, so may be able to travel a long way in the air currents. However, we would expect genetic isolation over the thousands of kilometres that separate the known populations of these plants.

Given both factors – that there are morphological differences between the plants, and that we expect there to be genetic isolation – we have considered naming the South African material as a separate species, after South African bryologist Sarie Perold, whose publication “Studies in the Sphaerocarpales (Hepaticae) from southern Africa. 1. The genus Monocarpus and its only member, M. sphaerocarpus” is a meticulously detailed piece of work.

However, in order to really understand Monocarpus in South Africa, and decide whether it represents a new species or not, we need to get hold of a bit more material and try some other investigations, including DNA analyses. Perold (1999) got the plant’s South African location from Australian botanist Hellmut Tölken, who had originally found it, and made several trips trying to recollect it; bryologist Terry Hedderson has also been keeping an eye open for samples. But no further material has been forthcoming: the site from which it is known has been developed, and now contains a hotel. And, unfortunately, the Monocarpus specimen from South Africa is scanty. Most of the collection, which was sent out as a loan from the Bolus Herbarium in Cape Town to the National Herbarium, Pretoria (PRE), has, according to T. Trinder-Smith, been lost. All that remains are some fragments of the original collection that were gifted to the National Herbarium of Victoria (MEL), and that we currently have on loan here in Edinburgh:

Monocarpus sphaerocarpus herbarium specimen, photograph by Tiina Sarkinen

Monocarpus sphaerocarpus herbarium specimen, photograph by Tiina Sarkinen

Unless the plant is rediscovered in South Africa, further study of the taxon there is impossible, given the size and fragility of the dust-like remaining specimen (shown in its entirity in the photograph above), as is molecular work to look for genetic differences between Australian and South African material.

It would be unfortunate, though, if the eradication of its only known site caused the extinction of a distinct South African species even prior to its formal description, which in itself is rendered impractical by the loss of nearly all of the existing plant material.

 

Monocarpus heading

 

 

References

Proskauer J (1961) On Carrpos I. Phytomorphology 11, 359-378.

On Monocarpus – http://stories.rbge.org.uk/archives/17112

Finding Monocarpus, in the Herbarium – http://stories.rbge.org.uk/archives/17146

Finding Monocarpus, in the field – http://stories.rbge.org.uk/archives/17272

Nov 022015
 

Although the exact relationships between the earliest land plant lineages are not yet well resolved, there is consensus that liverworts are one of the most ancient land plant groups. We are also confident that liverworts are a “good” taxonomic group, united by morphological and structural similarities, as well as by analyses of molecular sequence data that show that the entire group shares a common origin.

Fig 1a, Villarreal et al. 2015: molecular branch lengths across the liverwort tree of life

Fig 1a, Villarreal et al. 2015: molecular branch lengths across the liverwort tree of life, based on sampling in Laenen et al. 2014.

However, as a group, liverworts encompass a lot of variation – for example, some have leaves, some don’t; some have specialised sexual branches, others don’t; some grow in water, some on leaf surfaces, some on rocks; some are green, some red or brown, some closer to black… A less familiar metric that also varies across the liverworts is the rate of evolution of different parts of their genomes. Strikingly, complex thalloid liverworts have slow rates of molecular evolution for both the plastid and mitochondrial organelles. (In the figure on the left, they are the lineage represented in brown.)

While this phenomenom has been commented on by various authors over the years (e.g. Forrest et al. 2006), hard data has been lacking. Given the amount of sampling that we have for the complex thalloids, we have finally been able to put a number on it: We have calculated the rate of molecular evolution for the plastid to be 2.63 x 10-10 (SD 4.6 x 10-12) substitutions per site per year, based on coding sequences from atpB, psbA, psbT-psbH, rpoC1, rbcL and rps4, and the mitochondrial rate to be 5.31 x 10-11 (SD 9.4 x 10-13) substitutions per site per year, based on coding sequences from nad1, nad5 and rps3. The absolute mean substitution rate for the nuclear large ribosomal subunit (26S) is faster, at 7.76 x 10-10 (SD 1.4 x 10-11) substitutions per site per year.

In contrast, for the sister group (most other liverworts, shown in green in the figure), the calculated plastid rate, based on rbcL, is over three times higher than that for the complex thalloids, at 9.0 x 10-10 (Feldberg et al. 2014).

Bainard et al. 2013, Fig 1: Parsimony reconstruction of nuclear genome size evolution in liverworts (blue = small, red = large)

Bainard et al. 2013, Fig 1: Parsimony reconstruction of nuclear genome size in liverworts (blue = small, red = large)

However, seeing that there is a difference is the easy part; finding an explanation that fits the pattern is quite something else. Why would orgenellar genes evolve more slowly in the complex thalloids than in Haplomitrium, Treubia, the simple thalloid clades or the leafy liverworts? Could it tie in with a phenomenom known as RNA editing that is common to most liverwort lineages, but lacking in the complex thalloids? Do complex thalloids have longer generation times than the other liverworts, or slower metabolisms? On average, complex thalloids also seem to have smaller nuclear genomes than other liverwort lineages, although this is a broad generalization, with comparatively few genomes measured.

While we came up with some speculations in our last paper, we certainly don’t yet have an answer!

New Phytol title