Tag Archives: Taxonomy

Hitting the right target: taxonomic challenges for, and of, plant invasions

Primroses (genus Oenothera) are one of the group where it is difficult to align taxa invasive in Europe to their native North American counterparts.

Primroses (genus Oenothera) are one of the group where it is difficult to align taxa invasive in Europe to their native North American counterparts.

Taxonomic resources are essential for the effective management of invasive plants because biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa, and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches to improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. In a recent review in AoB PLANTS, Pysek et al. explore how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. They also explore how the taxonomic endeavour could benefit from studies of invasive species.

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Reasons to be cheerful (Parts, 4…)

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Backward-looking retrospectives [is there any other kind? – Ed.] are great. And that from the International Institute for Species Exploration at Arizona State University is one of the best. Annually, it publishes its list of the Top 10 new species discovered in the preceding year. Whilst this column has previously bemoaned the paucity of plant-based entrants in prior year’s lists, it is pleased to share news that there are four botanical worthies in the 2012 listing. And the list’s pedigree is unimpeachable because the committee members – who pick the ten – were ‘free to use any criteria they wished, keeping in mind the purpose of the Top 10 is to draw attention to biodiversity and the science and institutions engaged in its exploration. They were also encouraged to pay attention to taxonomic, geographic, and natural history diversity’. Their Top 10 includes Viola lilliputana, known from a single locality in the dry puna grassland ecoregion in the Peruvian Andes. At barely 1 cm (10 000 µm!) tall, the Lilliputian violet is a tiny miracle of nature and hard to spot, which may help to protect it from the over-zealous attentions of ‘collectors’ and agriculturalists who have all but extirpated the African violet from the wild. Also in the list is Eugenia petrikensis from Madagascar, whose uniqueness is ‘its rare occurrence, a large shrub with its beautiful bunch of flowers hanging on its branchlets’. However, I think it’s there because its leaf venation is brochidodromous*. Also in the list is Ochroconis lascauxensis which was isolated from ‘black stains’ in the Lascaux Caves in south-western France. Yes, I know it’s not a plant – it’s a fungus – but since fungi are non-animals, that’s good enough for this column (and, anyway, fungi are covered by the same ‘taxonomic code’ as plants; so, Botanists: 3, Others: 0, I think!). Finally – and I know all true botanists will appreciate this – also claimed for us chlorophytes is Juracimbrophlebia ginkgofolia, a new fossil species – a ‘hanging-fly’ – from Middle Jurassic deposits in the Jiulongshan Formation (in China’s Inner Mongolia). Yes, I know it’s an insect, but it was found with preserved leaves of a ginkgo-like tree, Yimaia capituliformis (presumably not Y. juracimbrophlebia-similiformis since I expect the plant was named first…), which it looks remarkably similar to (hence its specific epithet…)! What, an insect that wants to be a plant? How cool is that! And therefore thoroughly deserving of the honorary plant status I’m happy to accord it. What of the other organisms in the 2012 Top 10? Just some animals – sorry. However, what about a ‘spective’? A look-forward, where we second-guess the weirdest organisms we can imagine being discovered in 2013 (or beyond). What sort of plants would you propose? But if a single year’s list is too tame for you, you might like to know that the RHS’s (the UK’s Royal Horticultural Society) Plant of the Centenary is Geranium Rozanne (‘Gerwat’).

[* This sounds much more impressive than it is; brochidodromous venation means that ‘with a single primary vein, the secondary veins not terminating at the margin but joined together in a series of prominent upward arches or marginal loops on each side of the primary vein’, i.e. second-order veins are joined (there’s a good diagram thereof in Fig. 2A of Anita Roth-Nebelsick et al.’s 2001 review of the evolution and function of leaf venation architecture). And, yes, I know Saintpaulia isn’t a true violet, but it’s ‘literary licence’; so, no letters telling Mr P. Cuttings off, please! – Ed.]

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Australia’s national flower is an invasive species – even in Australia

Phylogeography of invasive Acacia

Phylogeography of invasive Acacia

Australia’s national flower, Acacia pycnantha (the golden wattle), is native to New South Wales, Victoria and South Australia. And very pretty it is too. But this species was introduced and has become invasive in Western Australia and is probably naturalizing in some areas of New South Wales and South Australia from cultivated plantings in revegetation projects and along roadsides. A. pycnantha is also an invasive species in the Eastern and Western Cape Provinces of South Africa, in Portugal, and possibly in California.

Understanding botanical introduction and invasion histories has important practical implications. The selection of effective host-specific biocontrol agents for invasive plants can depend on identifying which subspecific entities of the plant were introduced. Following the success of other biological control agents against Australian acacias in South Africa, a gall-forming wasp and a seed-feeding weevil have been used to try to control the plant.

A recent paper published in Annals of Botany aims to place invasive populations of Acacia pycnantha in the context of historical biogeographical patterns in the native range of the species in south-eastern Australia. The authors use plastid and nuclear DNA markers to reconstruct phylogenetic relationships among invasive and native populations, and to compare genetic diversities in these invasive and native populations. They show that the invasive genotype found in South Africa is similar to the invasive genotypes in Portugal and Western Australia and thus introduction of the same variant of gall-forming wasp successfully used for biological control in South Africa is recommended.

 

Elucidating the native sources of an invasive tree species, Acacia pycnantha, reveals unexpected native range diversity and structure. (2013) Annals of Botany 111 (5): 895-904. doi: 10.1093/aob/mct057
Understanding the introduction history of invasive plant species is important for their management and identifying effective host-specific biological control agents. However, uncertain taxonomy, intra- and interspecific hybridization, and cryptic speciation may obscure introduction histories, making it difficult to identify native regions to explore for host-specific agents. The overall aim of this study was to identify the native source populations of Acacia pycnantha, a tree native to south-eastern Australia and invasive in South Africa, Western Australia and Portugal. Using a phylogeographical approach also allowed an exploration of the historical processes that have shaped the genetic structure of A. pycnantha in its native range. Nuclear (nDNA) and plastid DNA sequence data were used in network and tree-building analyses to reconstruct phylogeographical relationships between native and invasive A. pycnantha populations. In addition, mismatch distributions, relative rates and Bayesian analyses were used to infer recent demographic processes and timing of events in Australia that led to population structure and diversification. The plastid network indicated that Australian populations of A. pycnantha are geographically structured into two informally recognized lineages, the wetland and dryland forms, whereas the nuclear phylogeny showed little geographical structure between these two forms. Moreover, the dryland form of A. pycnantha showed close genetic similarity to the wetland form based on nDNA sequence data. Hybrid zones may explain these findings, supported here by incongruent phylogenetic placement of some of these taxa between nuclear and plastid genealogies.
It is hypothesized that habitat fragmentation due to cycles of aridity inter-dispersed with periods of abundant rainfall during the Pleistocene (approx. 100 kya) probably gave rise to native dryland and wetland forms of A. pycnantha. Although the different lineages were confined to different ecological regions, we also found evidence for intraspecific hybridization in Victoria. The invasive populations in Portugal and South Africa represent wetland forms, whereas some South African populations resemble the Victorian dryland form. The success of the biological control programme for A. pycnantha in South Africa may therefore be attributed to the fact that the gall-forming wasp Trichilogaster signiventris was sourced from South Australian populations, which closely match most of the invasive populations in South Africa.

 

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Plastid and nuclear variation among apomictic polyploids

Plastid and nuclear variation among apomictic polyploids`

Plastid and nuclear variation among apomictic polyploids

Apomicts (plants grown from seeds or spores are produced without fertilization) account for 20–50 % of all species in northern Europe, but both phylogeny and evolutionary processes in apomictic genera remain largely unknown. Tyler and Jönsson use chloroplast sequences and nuclear microsatellites to create an overview of the variation in one of the most species-rich of all plant genera, Hieracium sensu stricto (hawkweed; Asteraceae). Although they find that cpDNA show too little variation and microsatellites are too variable to resolve relationships among species or evolutionary processes, they conclude that both species and sections as defined by morphology are congruent with the molecular data, that gene flow between the sections is rare, and that the tetraploid species may constitute the key to understanding evolution and speciation in Hieracium.

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Chlorophyllous catwalk… (Or, Hemerocallis, the ‘lily’ whose day has come?)

Image: José Goulão/Wikimedia Commons.

Image: José Goulão/Wikimedia Commons.

Question: what have Arabidopsis thaliana, Lotus japonicus, Zea mays, Lemna gibba and Hemerocallis got in common? Answer: they’re all model plantsnon-human species that are extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms.

OK, maybe not yet in the case of Hemerocallis, but a very strong – and overwhelmingly compelling? – case for its elevation to that exalted status has been made by María Rodríguez-Enríquez and Robert Grant-Downton. Maybe somewhat presciently, Hemerocallis (the daylily) is apparently often called ‘the perfect perennial’. And there are many good reasons why H. should be accorded model organism status. The two particularly highlighted by the paper’s authors are the strict developmental control of flower opening and flower senescence (programmed cell death, PCD), and its self-incompatibility (SI) system (SI is a general name for several genetic mechanisms in angiosperms that prevent self-fertilization and thus encourage outcrossing). In the words of its most fervent supporters, ‘New insights into fascinating subjects such as PCD, SI systems and the cellular, molecular and genetic basis of morphological innovations could be generated by exploration in this genus.

Equally, more applied studies, such as identifying and studying molecules of potential biomedical importance, would be assisted by embracing Hemerocallis as a model organism. Its impact as a future model will be enhanced by its amenability to cultivation in laboratory and field conditions… In addition, established methods for various tissue and cell culture systems as well as transformation will permit maximum exploitation of this genus by science… We look forward to a future where many more plant biologists are not only aware of, but also actively utilizing, Hemerocallis in research’.

Having reviewed the ‘manifesto’, as far as I can see the only thing against Hemerocallis’ formal adoption as a model plant (is there a committee that rules on such weighty matters? Should there be…?) – apart from the fact that the genus is in the really-hard-to-spell family Xanthorrhoeaceae (well, probably, for now – it seems that its family status is a little labile at present…) – is that it’s not arabidopsis. But neither is Lotus japonicus, nor Zea mays, nor Lemna gibba… And – but not that looks should count for anything – it will certainly look prettier in the lab than arabidopsis (and it is ‘full-size’, not scale-model size)! So, and anyway, Hemerocallis gets my vote!

[If there are deemed to be too many model plants, perhaps organisms should be in place for a 5-year term, and then have to be put up for re-election. How that might change the grant-awarding landscape! – Ed.]

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Plight of Plant taxonomy and taxonomists in India: What, Why and How?

An entry by R. Siva and S. Babu of VIT University.

The identifiable Aeschynanthus radicans

If you can’t identify Aeschynanthus radicans how can you do science? Photo: Jacinta Lluch Valero/Flickr

Plant Systematics involves the recognition, comparison, classification and naming the millions of plants that have existed and exist at present on the earth. India is rich in plant diversity and possesses almost 7% of the world’s flowering plants.1 In addition, India has a relatively good number of bryophytes (approximately 3000) and pteridophytes (approximately 1400). Most of the plants reported in India are based on the work of British taxonomists like Hooker or Gamble. The fact is that India lacks expertise in the field and there is a scarcity of knowledgeable taxonomists in India. At present, there could be only few ‘finger-countable’ plant taxonomists in India, the country where vast reserves of flora are yet to be studied. Many legendary plant taxonomists are either no more or retired with no replacement. The sporadic and limited studies on taxonomy in India are mainly oriented towards angiosperms. Cryptogams are long neglected from both taxonomical documentation and research exploitation

This subject has failed to attract the young researchers. One reason could be the educational system in India. Different branches of science are perceived not to have equal value. For instance, only few universities offer botany or zoology courses for graduate studies. If this situation persists, at some point in time, botany and zoology will have to be categorized as `endangered subjects’.2

There have been several earlier publications emphasizing on the fate of taxonomy and taxonomists in India3-5 as well as other parts of the world.6-7 Despite there has not been much change in the overall scenario. This has undoubtedly left a great deal of vacuum in this important field of taxonomy.

We propose the following as initial ways to change the present scenario in this aspect.

  1. Proper recognition of plant taxonomists in the form of awards and rewards.
  2. Specialized institutes on plant taxonomy in addition to Botanical Survey of India so as to make enough room for job opportunities.
  3. Introduction of plant taxonomy in the existing syllabi of undergraduate biology and biotechnology courses.
  4. Establishment of more number of research centres in the name of “Institute of Plant Biology”, with plant taxonomy focus.

Acknowledgments:

We sincerely thank Prof. Sean Mayes, Department of Crop Genetics, University of Nottingham and Prof. R. Uma Shaanker, University of Agricultural Science, India for their critical comments

References

  1. Ajmal Ali M. & Choudhary R.K. (2011). India needs more plant taxonomists, Nature, 471 (7336) 37-37. DOI:
  2. Siva, R., 2005. ‘Science becoming `endangered?’’, The Hindu, Education Plus, Oct. 31st.p 8.
  3. Dharmapalan B. (2001). Role of funding agencies for the betterment of taxonomy, Current Science, 81 (6) 629. PDF: http://www.currentscience.ac.in/Downloads/download_pdf.php?titleid=id_081_06_0629_0629_0
  4. Hariharan G.N. & Balaji P. (2002). Taxonomic research in India: Future prospects, Current Science, 83 (9) 1068-1070. PDF: http://www.currentscience.ac.in/Downloads/download_pdf.php?titleid=id_083_09_1068_1070_0
  5. Kholia B.S. & Fraser-Jenkins C.R. (2002). Misidentification makes scientific publications worthless – save our taxonomy and taxonomists, Current Science, 100 (4) 458-461. PDF: http://www.currentscience.ac.in/Volumes/100/04/0458.pdf
  6. Wägele H., Klussmann-Kolb A., Kuhlmann M., Haszprunar G., Lindberg D., Koch A. & Wägele J.W. (2011). The taxonomist – an endangered race. A practical proposal for its survival, Frontiers in Zoology, 8 (1) 25. DOI:
  7. Guerra-García J.M., Espinosa F. & García-Gómez J.C. (2008). Taxonomy today: an overview about the main topics in Taxonomy, Zoologica baetica, 19 15-49. URL: http://www.ugr.es/~zool_bae/vol19/Zoo-2.pdf

Photo: Aeschynanthus radicans by Jacinta Lluch Valero. This image licensed under a Creative Commons by-sa licence.

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Botany, a man’s world?

Image: Wikimedia Commons.

Image: Wikimedia Commons.

What do you make of this: ‘In the 18th century, not yet 30 years old, she became the first woman to travel around the world. Along the way she helped collect thousands of plant specimens, some of which were new species. And she did it all dressed as a man’?

Sounds incredible, I know but apparently it is true and relates to one Ms Baret (or Baré). To cut a long (but fascinating!) story short, a wrong – that no plant was named after this indefatigable plants-person – has now been righted by Eric Tepe et al. Their article entitled, ‘A new species of Solanum named for Jeanne Baret, an overlooked contributor to the history of botany’ formally describes Solanum baretiae Tepe, sp. nov. As the authors proudly declare ‘This species in [sic] named in honor of Jeanne Baret (1740–1807), an unwitting explorer who risked life and limb for love of botany and, in doing so, became the first woman to circumnavigate the world… a woman dressed as a man, a female botanist in a male-dominated field, and a working class woman who had travelled farther than most aristocrats’.

Fittingly, S. baretiae is a new member of a cosmopolitanly cultivated, well-travelled and important food genus, suitably befitting for such a cosmopolitan, well-travelled lady! And let us not forget that the genus – Solanum – includes S. tuberosum, the potato, which itself can be dressed up in many different guises, e.g. chips (aka ‘fries’ in the USA, ‘frites’ in France, and – allegedly – ‘Fritz’ in Germany), mashed potato, duchess potato, jacket potato and crisps (bizarrely called ‘chips’ in the USA). But cross-dressing, eh? I think I’d be cross if I had to dress as a woman to pursue my botanical passion; but if that’s what it takes… Hopefully, however, and nowadays, we are much more egalitarian and anybody with the appropriate aptitude can aspire to be a botanist. Though with scientific names like Phallus impudicus and Clitoria for organisms within the remit of the Melbourne Code, and what with that racy Scandinavian Mr Linnaeus’ overtly sexually charged plant classification system, maybe botany is not such a suitable pastime for the gentler sex – or those otherwise of a nervous or sensitive disposition…?

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Go Botany – Plant identification on a computer or tablet near you

Go Botany: the new site for New England Plant identification

Go Botany: the new site for New England Plant identification

First came Flora Novae Angliae, the definitive manual for the identification of native and naturalized vascular plants of New England. Now comes the website with thousands of full-color images and illustrations for teaching and learning botany.

Dr Elizabeth Farnsworth has told us about the New England Wild Flower Society’s announcement of the first stage of Go Botany, the Society’s exciting, new open source website that teaches botany and plant identification, is now online.

She writes “Imagine a field guide at your fingertips that can help you learn about the native and naturalized plants of New England! Maybe you’re a teacher looking for new ways to interest your ninth-graders in learning about the natural world or a plant enthusiast looking to meet and share new finds with a community of neighbors with similar interests. Whether you’re a botanical beginner or an expert with this free Go Botany web tool, you can now identify 1,200 of the most common native and naturalized plants of New England. But there is much more to come.

Go Botany Homepage

Go Botany Homepage

With a $2.5 million grant from the National Science Foundation and other generous donations, we are building a suite of many learning tools. Our flexible, user-friendly interactive key will enable you to identify species based on whichever portions of the plant – leaves, flowers, winter buds, bark, etc. – you are able to observe at any given time of the year. Using truly innovative technology, this dynamic key asks you the questions about your plant that most efficiently help you hone in on your species, based on the questions you have already answered. Our Simple Key will help you identify 1,200 of the more common New England plants. If you prefer to use a more traditional dichotomous key, later in 2012 Go Botany will feature an innovative, clickable key that is easier to navigate than a conventional field guide – no more flipping pages! Also coming in 2012, is the Full Key, which covers more than 3,500 plant species, including subspecies and varieties. We are also developing an online, collaborative portal called PlantShare, where you can join a community of plant enthusiasts and create and share checklists and photographs of species you have seen. Have a question? Here’s your chance to ask a botanist. Our research botanist and assistants will be available to answer all your questions.

Go Botany is fun and friendly. Jargon is kept to a minimum, but all botanical terms are linked to a pop-up glossary. Drawings illustrate all the characteristics in the key. Once you identify your plant, you can see a wealth of information about it, including gorgeous color photographs, maps of its geographic range, diagnostic characteristics, and memorable facts. The Go Botany design is optimized for both desktop and tablet computers, so you can use it anywhere you have a web connection.

Why the web? New England Wild Flower Society recognizes that the future of science education relies, in part, on using new technologies effectively to convey information, excite curiosity, point learners to related resources, and enable them to use portable devices to identify species in the field. At the same time, we know technology must go hand-in-hand with mentoring and human interactions that introduce new concepts and reinforce learning in a memorable and meaningful way. The web is a vast repository of useful data and images of plants, but you cannot experience the excitement and fascination of observing plants in the wild by surfing the web. Thus, we want to combine the rich information available on the web with interactive data-sharing and networking tools to make botanizing an active, participatory process. Botany isn’t just for plant geeks anymore!

Go Botany can be tailored to any locality or region with a documented list of plants. Thus, we are working with three institutional partners – Montshire Museum of Science (Vermont), Chewonki Foundation (Maine), and the Peabody Museum of Natural History (Connecticut) – to develop online floras for their unique settings. The Montshire Museum will feature a guide to plants of their Woodland Trail, as well as a colorful, interactive kiosk called “Hemlock Holmes” that challenges kids to identify mystery plants. Students attending the Semester School at the Chewonki Foundation will use Go Botany to document the flora of Chewonki Neck and several Maine islands. The Peabody Museum of Natural History will engage urban students in identifying plants at their new West Campus in New Haven, CT. These organizations attract a diversity of audiences, and we are developing Go Botany with lots of built-in flexibility to appeal to a range of users. To introduce Go Botany and encourage its widespread use in both the classroom and the field, we will conduct dozens of teacher-training workshops throughout the region and at national meetings in 2012-13. Teachers will be able to share the many ways they have used Go Botany, posting their curricula and modules in the Resources section of the website.

Plant identification on line

Plant identification on line

Why stop at New England? Go Botany is a model that can be exported nationally to any institution that seeks to develop an interactive flora and educational website tailored to their region. Thus, for example, we are collaborating with scientists at the Smithsonian Institution, who will use our software to develop an interactive key to the orchids of North America! Many organizations, from universities to land trusts, are expressing interest in adapting the innovative Go Botany software to their local floras. We are also hosting a session on next-generation field guides at the Ecological Society of America national meetings this summer, bringing together other high-profile innovators of web technology such as eBird, DiscoverLife, BugGuide, and LeafSnap.

The Go Botany project is the product of many hands working hard over the past two years, including the computing firm Jazkarta (Boston, MA), smart programmers from as far away as Newfoundland and Los Angeles, seven botanical data specialists, four image collectors, a creative design team at Fresh Tilled Soil (Waltham, MA), a talented User-experience designer (Matt Belge, VisionLogic), and many Society staff members and interns who have starred in helpful videos, photographed plants, and beta-tested the web application. The whole project is being objectively assessed by the Lesley University Program Evaluation Research Group, which is making sure we reach our goals of enhancing botanical education. We’re grateful to the many photographers who have kindly donated plant images and many other collaborators and advisors; we’ll be looking for your input and suggestions, too!”

Ready? Set? Go to: http://www.newenglandwild.org/gobotany

New England Wildflower Society

New England Wildflower Society

The mission of New England Wild Flower Society is to conserve and promote the region’s native plants to ensure healthy, biologically diverse landscapes. Founded in 1900, the Society is the nation’s oldest plant conservation organization and a recognized leader in native plant conservation, horticulture, and education. The Society’s headquarters, Garden in the Woods, is a renowned native plant botanic garden in Framingham, Massachusetts, that attracts visitors from all over the world. From this base, 35 staff and more than 1,000 volunteers work throughout New England to monitor and protect rare and endangered plants, collect and preserve seeds to ensure biological diversity, detect and control invasive species, conduct research, and offer a range of educational programs. The Society also operates a native plant nursery at Nasami Farm in western Massachusetts, which grows plants for retail customers and for landscaping and restoration projects, and has eight sanctuaries in Maine, Massachusetts, New Hampshire, and Vermont that are open to the public.

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Answer: Not Lamarck(!)

Answer: Not Lamarck(!)

Answer: Not Lamarck(!)

OK, that’s the answer, what was the question? Who invented the dichotomous key for identification? Well, as anybody who has taught students about keys and their use as tools for plant ID (or even for animals if you must!) will probably agree, the consensus is that the oft-derided French former botanist Jean-Baptiste Lamarck is credited with that honour, in 1778 (although curiously – presciently? – this factoid is not mentioned on Lamarck’s ‘official’ biography on Wikipedia). Well, Lawrence Griffing in his beautifully illustrated Special Paper makes a compelling case (this Englishman is convinced, anyway!) that the real credit belongs to Brit Richard Waller , in … 1689! I’m sure the French may not agree, but in that time-honoured British tradition of compromise (and trying to maintain some semblance of cordiale in the oft-strained trans-manche entente), how about this: Lamarck keeps credit for the first text-based dichot key, but Waller gets the kudos for the first image-based one?

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