This is an overview of the Flora of China Project, its digital resources, and a look at possible avenues for future floras.
A flora refers to plants of a particular place, and to the publication of descriptions about those plants. Two examples include the Flora of North America and Flora of China.
These floras include classifications, keys for identification, scientific and common names, synonymies, descriptions, flowering and fruiting times, distributions, and comments about plant uses, conservation, and more.
The Flora of China is a collaborative project to publish the first modern English-language treatment of the ca. 31,500 species of vascular plants of China. It includes 24 text volumes, 24 accompanying illustration volumes, plus an introductory volume.
In order to get to the current Flora, first, let’s go back in time to see the formation of knowledge about the plants of China. Significant collecting began in the late 1800s to early 1900s. Here at Harvard, Asa Gray was the recipient of many specimens from early expeditions; influenced by Asa Gray, Charles Sargent set about to introduce Asian plants to the Boston environment and to bring back specimens to the herbarium. E. H. Wilson brought back seeds, specimens, and photographs. Other collectors included Joseph Rock, C. K. Schneider, T. T. Yu, R. C. Ching, W. P. Fang, and many others.
The type specimen of Sorbus rehderiana collected by E. H. Wilson in 1908, and a recent 2006 specimen collected by Dave Boufford and his team in Zhongdian Xian, Yunnan.
As they studied these collections, botanists began publishing extensive catalogues, notes, and monographs about the plants of China. For example, these titles by Bretschneider, Hector Léveillé, Handel-Mazetti, H. H. Hu and R. C. Ching, and E. H. Wilson.
The first volume of the Chinese-language Flora Reipublicae Popularis Sinicae was published in 1959, and was completed in 2004, amounting to 45 years, 80 volumes in 125 parts. Begun in 1988, the Flora of China is a modern revision, not simply a translation, and is scheduled for completion in 2013, amounting to 25 years from start to finish. We’ll look at possibilities for a next edition later in the talk.
Although China has about the same land area and latitude as the contiguous United States, there are about twice as many species as the US and Canada combined. Of the 31,500 species, ca. 29,200 are seed plants accounting for 93% of the flora, and the ferns and their allies account for the remainder. There are about 7500 species of trees and shrubs, and about 8000 species of economic importance.
Approximately half of China’s seed plants are endemic to China.
So far, 22 text volumes have been published (with another two treating the pteridophytes next year, and the introductory volume in 2013). Twenty illustration volumes have been published with the remaining four by 2013. Volume 1 will present a history of the project, statistics about the flora and authors, comparison of classification systems, major corrigenda, new or overlooked taxa, nomenclatural novelties, and indices to names.
Here is a look at some of the largest genera of plants in China. For example, Rhododendron the most species-rich genus with 571 spp., and other woody representatives (of interest to the Arboretum here) including Salix with 275 spp, Berberis 215 spp., Rubus 208 spp., Ilex 204 spp., Lithocarpus 123 spp., and Acer and Ficus each with 99 spp.
Editorial centers in China include those in Beijing (a coordinating center), Kunming, Guangzhou, and Nanjing; and those outside of China include Missouri Botanical Garden (a coordinating center), Royal Botanic Gardens in Edinburgh and Kew, the California Academy of Sciences, the Smithsonian, Paris, and Harvard. With their extensive collections and libraries, and fascinating histories of exploration and research, the Harvard Herbaria and the Arnold Arboretum serve as an important Center for the Project.
Treatments of families are first prepared by Chinese authors, often the same authors as for the Chinese edition Flora Reipublicae Popularis Sinicae, edited according to the Project’s guidelines, and then the drafts made available online at this early stage.
The manuscripts are shared with non-Chinese specialists for collaborative revision, reviewed by other specialists, and corrected and edited again.
Finally, the volume is formatted, proofread, and published as a printed volume, PDFs of the family treatments are provided online, and the treatments added to a database for online browsing and searching via eFloras.org, which we will look at in a moment.
Here is an example of an original draft requiring some editing.
And here is that same draft in edited form, using revision marks to track changes.
Coauthors usually use revision marks on electronic copies of the manuscript files, but there are a few who sent their corrections handwritten via air mail, in this case Charles Jeffrey as mailed from Russia.
Similarly, other specialists have reviewed manuscripts and provided their suggestions usually with revision marks in word processed files. However, we have received suggestions for improvements in other forms from time to time. For example, this sketch is from Michael Donoghue at Yale University, in which he guided the re-alignment of the treatment of the families in the Dipsacales, separating the actinomorphic, regular flowers of Viburnum and its relatives as Adoxaceae, from the zygomorphic, irregular flowers of Lonicera in the Caprifoliaceae and related families.
which of course, reminds us of the famous “tree of life” sketch by Charles Darwin.
Finally, text volumes of family treatments and accompanying illustration volumes are published.
New names and combinations are regularly published in journals such as Novon, Annals of Missouri Botanical Garden, Harvard Papers in Botany, and the Journal of Systematics and Evolution (formerly Acta Phytotaxonomica Sinica), while others have been published in the Flora of China itself.
The Flora of China Checklist is part of the Tropicos database system at Missouri Botanical Garden. Records in Tropicos are routinely linked to the FOC Illustrations, type images, specimen data and images, J-STOR, the International Plant Names Index, Botanicus and Biodiversity Heritage Library protologues.
As many of you know, Dr. Hu Shiu-ying was here at Harvard for many years and is now living in Hong Kong at 101 or 103 years old. In the 1950s, Dr. Hu and several assistants searched the botany libraries for all the names that had been used for plants of China, and prepared an index file of these names. These 158,000+ cards were digitally scanned and the card images are available online.
The Hu Card Index is especially useful for locating approximately 9000 infraspecific names; infraspecific names were not included as part of the Index Kewensis until 1971.
The Flora of China website is located at www.foc.org, and includes information about the Project’s structure and resources. The website serves as an entry path to the floristic treatments, illustrations, and links to further taxonomic resources.
Electronic versions of several floras (“eFloras”) associated with Missouri Botanical Garden, including the FOC, are publicly and freely available online via a web interface, www.eFloras.org (developed by Hong Song, originally of MO but now at St. Louis University). The web interface enables browsing and searching of the centralized, relational database containing the published treatments. We can browse by volume, family, and so on; and search by name alone, or in combination with distributional data about elevation, province, and adjacent country.
Here is an example of a search for spruce, Picea in Sichuan.
And the resultant hyperlinked list of 6 species and their varieties.
Taxon records are linked to related objects. Here is an example of a related object link to this color illustration of Rhododendron leptocladon which serves as the frontispiece to Volume 14.
One of the related links takes us to this nomenclatural record in the Tropicos database.
And this related link takes us to the IPNI record for the same taxon.
The FOC illustrations are linked to their respective treatments. For example, this one of Ginkgo biloba in volume 4.
and this one of Liriodendron chinense in volume 7, originally published by Sargent.
Acer griseum in Volume 11.
Zanthoxylum simulans, Chinese prickly-ash or better known in Chinese cooking as Sichuan peppercorn, in Volume 11.
Another Rhododendron, this one named by Rehder and Wilson in Sargent’s Plantae Wilsonae.
And an interesting bamboo, Phyllostachys aurea.
And of course, the orchid volume draws a lot of attention. Here’s one of Cypripedium tibeticum.
In addition to the FOC illustrations, there are links to photos, such as from Dave Boufford’s Biodiversity of the Hengduan Mountains Project (As you may know, Dave will be presenting a seminar here in January). Here’s one of Lithocarpus confinis in the Fagaceae.
The creeping habit of Salix souliei.
The clear light blue Corydalis curviflora.
A star-like anise, Illicium simonsii.
and Viburnum kansuense.
Since the Flora of China will have taken 25 years from start to finish, there have been several (709) corrections needed and new (648) names appeared along the way. Here is one of Pinus fragilissima that was published after the printed volume 4.
The data are regularly updated with “post-publication” names, which appeared after the production of the printed volume, and errors corrected via a web form. The web form allows us to update and add records. So the data have been added for the previous slide, including a link to a PDF copy of the scientific paper containing the protologue.
In addition to the synoptic descriptions of the taxa, Floras contain dichotomous keys as identification tools. The identification process must follow a pre-defined path. At each step, asking does the plant have traits A or B?
Each lead of a couplet ideally provides contrasting, diagnostic characters.
However, there are problems. Sometimes, there are long intervals between the first and second halves of a couplet.
Secondly, if the diagnostic character is unavailable, it is sometimes impossible to use this type of key for identification.
Here is an example of a key with a long interval between 1a and 1b. In fact, 1b doesn’t even make it to this slide.
Bracketted keys provide a solution for these situations, particularly for the web, so when the treatments are added to eFloras, the dichotomous keys in the FOC are routinely converted to bracketted keys, and hyperlinked to the respective taxon pages.
Sometimes, the diagnostic character is unavailable, for example, a fruiting character but no fruit can be found.
Interactive identification keys provide a solution, enabling multi-access, to select available characters for identification.
Interactive keys can include images of character states to aid selection.
Interactive keys can include images of taxa for comparison, whether they be illustrations, scans, or photos.
Interactive keys to large genera for the Flora of China are available online. These are available in a standard DELTA Intkey format. DELTA can be used locally or remotely. Output options from DELTA include interactive keys, data summaries, natural language descriptions, keys, and distance matrices.
These same keys are available with another interactive key program, NaviKey, since NaviKey uses the same basic DELTA files (chars, items, and specs), and can be used on any platform.
Although DELTA was formerly limited to Windows, the new Open DELTA program is platform-independent.
Here are the two different views for entering and editing data using the DELTA Editor. On the left is the tree view, providing a list of items (or taxa), plus a list of characters, and their associated character states. On the right is the grid view, displaying a typical spreadsheet data form.
Here is a DELTA Intkey to families. For example, we can select leaves opposite.
and 144 possible families remain; 130 families are eliminated.
We can continue to select further character states, for example, leaves opposite, margin lobed, fruit type samara, and plant habit tree, and four families remain including the Aceraceae.
Within an Intkey to the Aceraceae, we can select tree, leaf lobes 3, samara wings spreading obtusely, and distribution Yunnan, and 9 taxa remain.
If we compare the remaining taxa, one of the differences between them is elevational distribution, and here, 3575 meters would suggest a possible match with Acer forrestii.
Similar to DELTA Intkey, here is screenshot of the NaviKey applet online.
and as a stand-alone on a local computer.
Here is a view of the new Open DELTA Editor, for entering data. For example, leaf lobes 3, 5, or 7 were entered for this tree.
And a view of the new Open DELTA Intkey from the same dataset, with its use in identification.
As we have seen with DELTA, descriptions themselves are essentially archives of data recorded and measured by botanists. Databasing the descriptions will enable statistical summaries about plant structures which can be used by biologists. The data trends and statistics may lend insights into plant biological structures & functions, development & evolution, ecology and biodiversity. M arking up descriptions with XML tags (and thus into data fields) is being explored by Hong Cui, a professor of information technologies, at the University of Arizona and her students.
Here is an example, using Hong Cui’s interface to search for evergreen shrubs with linear leaves with a possible result of Taxus.
Now that the Flora of China is nearing completion, it is timely to consider a digital extension of the flora into the future.
The future holds the potential for both dynamic and multilingual, digital floras. Tropicos will serve as the database for maintaining and updating “eFloras” with all of its current functionality. Descriptions and distributions can be more finely parsed into data fields. Further images will provide useful identification guides, as well as improving and extending interactive keys.
Now that we have these data, we can ask questions about distributions, ecology, development, and evolution. Using the DELTA summary program, we can get a species count per province, elevational distributional information, and morphological statistics such as leaf petiole length.
Using the distribution matrix function in DELTA, we can output the data in a form to produce trees or cladograms (based on morphological data), which specialists can utilize in combination with new molecular data to examine and better understand relationships. For example, this one of the Aceraceae.
And this one of the Betulaceae.
Unfortunately, descriptive data are missing, incomplete, or inaccurate for a large number of taxa. To be most useful, additional specimens will have to be analyzed and measured and the data recorded to make the data in DELTA, or in another interactive program, precise enough for accurate identification. Checking collections to fill-in missing character states and measurements will improve interactive keys.
Databasing collections will improve our knowledge and understanding of distributional ranges. If the Flora of China taxa are linked to specimens, and the specimens georeferenced, it will be possible to generate an accurate map of each species, based on actual specimens, by just pushing a button directly from the species description.
Now that electronic devices are becoming commonplace, it is timely to create new tools for scientific researchers, students, and the curious public, to identify plants, and to ask questions about their names, characteristics, distributions, ecology, and uses. A person should be able to use the Flora anywhere, from a desktop to a handheld device carried into the field and, knowing where in China he or she is, be able to identify any plant using easily observed features of the plant. Eventually, even the morphology and color of a flower from a photo taken in the field with a smart phone or other device could be compared with photos and colors of flowers stored in the database for each taxon. The possibility of having a truly modern, dynamically growing Flora is a real possibility, especially if the Flora of China were used as a foundation. If it were built upon and continuously updated it would become almost immediately a reliable, indispensable and invaluable asset to researchers everywhere.
PathKey is a new interface for accessing interactive identification keys in DELTA format on any browser or mobile device. It was just developed by Hongping Liang of Connecticut. It is a web-based application, which is accessible from any web browser or mobile device, e.g., IPhone, IPad, Android, etc. Features: Accessible from any browser; Optimized for mobile devices, e.g., IPhone, IPad, Android Phones; No program needed to install, no applets required; Offline access for field use; Easily linked from any web site.
I thank my fellow Flora of China collaborators, persons here at Harvard: Dave Boufford, Anne Marie Countie, Brian Franzone; in St. Louis: Hong Song, Myriam Fica and Chris Freeland, and many others. The Flora of China Project has been made possible thanks to support from the Arnold Arboretum, the Harvard University Herbaria, Missouri Botanical Garden, the Starr Foundation, and the National Science Foundation.
Finally, I would like to conclude with this final slide -- a photo of Hovenia dulcis taken by my father Paul at Highland Park in Rochester, NY. Thank you.
Flora of China: e-resources
Flora of China e-Resources Anthony R. Brach Editor, Missouri Botanical GardenAssociate of the Arnold Arboretum and Harvard University Herbaria
What is a Flora?• plants occurring within a given region (i.e., “flora”).• publication of scientific descriptions of those plants (i.e., “Flora”).
What is a Flora?• plants occurring within a given region (i.e., “flora”).• publication of scientific descriptions of those plants (i.e., “Flora”).• classification, identification keys, scientific and vernacular names, synonyms, descriptions, phenology, distributions, uses, conservation.
Flora of China Projecta collaborative project to publish the first modern English-language account of the ca. 31,500 species of vascular plants of China. 24 text volumes 24 illustration volumes plus introductory volume
Flora of ChinaFlora Reipublicae Popularis Sinicae (FRPS)• in Chinese• 80 volumes in 126 books• 1959–2004 (45 years)Flora of China (FOC)• in English: modern revision• 25 text volumes + 24 illustration vols.• 1988–2013 (25 years)
A few figures• Chinese vascular plants: ca. 31,500 spp.• China: about same land area and latitude as contiguous USA. About 2X as many as species as FNA.• Seed plants: 29,224 spp. (93% of flora)• About 7500 tree and shrub spp.• About 8000 spp. of economic importance• Pteridophytes: ca. 2,250 spp. overlay map from Dave Boufford adapted from Edgar Snow (ca. 1930s)
A few figures• Chinese vascular plants: ca. 31,500 spp.• Seed plants: 29,224 spp. (93% of flora)• Endemic seed plants: 14,753 spp. (50.5%)
A few figures• Volumes published and online:• 22 text vols. (+2 in 2012 + intro. in 2013)• 20 illustration vols. (+4 by 2013) Coming Soon!
The Harvard University Herbaria and Arnold Arboretum serve as an important Center for the Project.
Editorial Process• Draft prepared by Chinese author(s)• Edited according to FOC Guidelines (and draft online as HTML)
Editorial Process• Draft prepared by Chinese author(s)• Edited according to FOC Guidelines (and draft online as HTML)• Coauthored by non-Chinese specialist(s) -- collaborative revision• Corrected and edited• Reviewed by other specialists and regional advisors• Corrected and edited
Editorial Process• Draft prepared by Chinese author(s)• Edited according to FOC Guidelines (and draft online as HTML)• Coauthored by non-Chinese specialist(s) -- collaborative revision• Corrected and edited• Reviewed by other specialists and regional advisors• Corrected and edited• Volume formatted• Proofread• Published (PDFs online, printed volumes, added to eFloras.org)
Editorial process: Original draft• Acer leipoense Fang et Soong in Act. phytotax. Sin.11:179.1966• 雷波槭 lei bo qi• Acer leipoense var. leucotrichum Fang in Act. phytotax. Sin. 17(1):85, Pl.14:4.1979; A. longipedicellatum C.Y.Wu in Act. phytotax. 21 (3): 337.1983.• Tree to 8 m tall;bark deep brown, purple brown; branchlets round, those of the present year green or purplish green, pubescent, those of more than one year old brown, glabrous; winter-budes ovate, scales ciliate on the margin. Petiolesslender, glabrous, purplish green, 7-8 cm long; leaf deciduous chartaceous, roundish-ovate in outline, 9-11 x7-12 cm, subcordate or round at base, 3-lobed; shallowly and forwardly 3-lobed, the margin of lobes usually entire, rarely with a few serrations; upper surface green, glabrous; lower surface grey, powery and pebescent. Flower unknown. Fruits yellown, brown, in racemes 15-25cm long, purplish green, subglabrous, nutlets yellown brown. strongly convexed, 1 cm in diameter, pubescent; wing falcate, included nutlets 4-4.5 cm long, 1.5 borad. spreading right or acute angles. Fr. Sep.∀ •Open forest, 2000-2700 m, SW Sichuan.
Dichotomous keys• keys as identification tools• ID process must follow a predefined path, does the plant have traits “A” or “B”?
Dichotomous keys• keys as identification tools• ID process must follow a predefined path, does the plant have traits “A” or “B”?• Each lead of a couplet (e.g., 1a, 1b) provides contrasting, diagnostic characters.
Problems with dichotomous keys• For indented keys, sometimes long intervals between first and second halves of a couplet, require turning several pages or scrolling to a distant lead.
Problems with dichotomous keys• For indented keys, sometimes long intervals between first and second halves of a couplet, require turning several pages or scrolling to a distant lead.• If the diagnostic character is unavailable (e.g., fl., fr., or sterile specimens), it is difficult (or even impossible) to use this type of key.
Ex. 1 (Pinus): Long interval between 1a and 1b
Example 2 (Quercus): What if adiagnostic character is unavailable?
Solution 2: Interactive Keys• Multi-access (multiple entry)• not dependent upon few or single characters that may be absent
Solution 2: Interactive Keys• Multi-access (multiple entry) – not dependent upon few or single characters that may be absent• can include images of character states (to aid selection)image from Radford et al.http://www.ibiblio.org/botnet/glossary/
Solution 2: Interactive Keys• Multi-access (multiple entry) – not dependent upon few or single characters that may be absent• can include images of character states (for selection)• can include images of taxa (for comparison)
Interactive Keys - Flora of China: interactive keys to large genera: 15000+ species (ongoing) DELTA• DEscription Language for TAxonomy• 30 years of development: CSIRO (Australia)• local use: stand-alone• remote use: web-accessible (with Intkey application)• output options: interactive keys: Intkey, data summaries, natural language descriptions, keys, distance matrices• formerly only Windows
Interactive Keys - Flora of China: interactive keys to large genera: 15000+ species (ongoing) DELTA Intkey NaviKey • local use: stand-alone• DEscription Language for application TAxonomy • remote use: applet on web• 30 years of development: server CSIRO (Australia) • uses same DELTA file• free for non-commercial use directives (chars, items, specs)• local use: stand-alone output from DELTA Editor• remote use: web-accessible • any platform (Java-based) (with Intkey application)• output options• formerly only Windows
Interactive Keys - Flora of China: interactive keys to large genera: 15000+ species (ongoing) DELTA Intkey NaviKey • local use: stand-alone• local use: stand-alone application• remote use: web-accessible • remote use: applet on web (with Intkey application) server• formerly only Windows • any platform (Java-based) new Open-DELTA Java • uses same DELTA file version in development: directives (chars, items, specs) Atlas of Living Australia: output from DELTA Editor platform-independent
Future: Digital FlorasElectronic publication: digital, dynamic florasNomenclature• Tropicos to maintain eFloras: current functionality – Post-publication updates (new names, corrigenda) – Infraspecific names into Tropicos & IPNI (from Hu Card Index and Fl. Japan)Descriptions and Identification• Databasing descriptions and distributions (XML and DELTA; bilingual flora; treating new taxa)• Images (specimens, living plants, distribution maps)• Interactive keys (improvements and extensions)
Compound-leaved Simple-leavedDistance Matrix from DELTA Data (Nexus format) e.g., Aceraceae Simple-leaved
CarpinusDistance Matrix from DELTA Data (Nexus format) e.g., Betulaceae Carpinus Ostrya Corylus Betula Ostryopsis Betula Alnus
Future: Record further data from specimens to improve Interactive Keys
Future: Database collection data for plotting distributions and improving interactive keys Most collections from Gaoligongshan, bordering Myanmar. Map prepared by Brian Franzone.
Future: Potential for App Development• Should be able to use the Flora anywhere.• Identify any plant using easily observed features of the plant.Having a modern, dynamically growing flora is a real possibility, with the Flora of China as a foundation.
Acknowledgments• Flora of China Project collaborators• Dave Boufford, Anne Marie Countie, Brian Franzone (Harvard)• Hong Song (St. Louis University)• Hong Cui (University of Arizona)• Hongping Liang (Connecticut)• Myriam Fica and Chris Freeland (Missouri Botanical Garden)• Arnold Arboretum• Harvard University Herbaria• Missouri Botanical Garden• Starr Foundation• National Science Foundation
Season’s Greetings!Hovenia dulcis Thunb. (Rhamnaceae) at Highland Park, Rochester, NY Photo by Paul J. Brach