Tuesday, 27 August 2013

Global Species Database Spotlight: World Ferns & World Plants

Global Species Database owner Michael Hassler 

Global Species Database name:
World Ferns / World Plants

Your name:
Michael Hassler 

Your position:  
Database owner
Where are the databases located?
On the servers of the Karlsruhe Institute of Technology Botanical Garden in Karlsruhe, Germany) 

What taxon/taxa do your databases cover?
All flowering plants, ferns and lycophytes of the world. 

How many species names do you hold?
13,384 plus 1,274 infraspecific taxa in World Ferns
ca. 350.000 in World Plants

How many synonyms?
42,448 in World Ferns
ca. 1.000,000 in World Plants 

How many common names?
1,189 in World Ferns
ca. 10,000 in World Plants 

How and when did the database come about?
In the late 1980's and early 1990's some interested people and collaborators in Germany (botanists and entomologists) discussed the possibility of using computer based technology to create world checklists. This was an age when all available checklists were paper based (for example Kew Index and Index Filicum) and many people were still using early home computer generations. The first example was a worldwide checklist of weevils (Joachim Rheinheimer) which was introduced in the mid 1990's and keeps growing today. When the first generation of Kew Index was available electronically, the project for the flowering plants was started. The goal was to use the data set of Kew Index and cross-check it to regional and local databases, floras and generic treatments to create a synonymic checklist with as many synonyms as possible and a complete distribution (Kew Index does not list distribution).  The whole project is unfunded and totally a volunteer work. As expected, the project needed more than 10 years for the initial stage and is now 20 years old. 

In the early 2000's two more projects were spun off: Firstly, scans of the Index Filicum (which never was available electronically) yielded an additional dataset for the Ferns and Lycophytes; and secondly, since we had photographs of several thousand species of Orchids, the Orchids were separated as a project in cooperation with the Heidelberg Botanical Garden. The Orchid Checklist was originally intended to be published on CD, but several reasons (sickness and death of a main contributor) as well as competition from Kew delayed the project for many years. Finally it was published on our website 2009 as "Illustrated World Compendium of Orchids".  

When Kew started to publish their World Checklist of Selected Plant Families (WCSP), having more resources available, the authors of World Plants decided that Kew would probably be faster than World Plants, and stopped work on World Plants. 

Finally, in 2013 it was decided to publish the 180,000 species or so (about 50 % of total) which are not yet covered by WCSP or others, in the context of Catalogue of Life.

World Ferns developed separately and with a higher priority since WCSP did not have a similar project for Ferns and Lycophytes. The first versions were published in 2002 together with Brian Swale on his New Zealand website. Since 2006, WorldFerns has a new home on the authors website on the KIT server (Karlsruhe Institute of Technology, Botanical Garden) and has been met with growing interest by the community as the leading Fern checklist and taxonomic reference. It does contain pictures of about 800 species (6 % of total).

Improving on WCSP and similar projects our databases - World Ferns and World Plants - do contain pictures (at least on our own website) and we aim to include as many as possible. Orchids have more than 5500 species in pictures, and Ferns more than 800. World Ferns and World Plants also maintain a proper taxonomic order for families and genera reflecting relationships within the tree (IPNI, WCSP, Index Kewensis and others are completely alphabetically based). Only within one genus does the database use an alphabetical approach.

How many people work on the database?
Currently just myself, but many collaborators regularly supply suggestions and updates.

What software do you use?
Data assembly is done on a text file basis. The standardised text files are converted into CSV format and proprietary software converts it into the website format.

How complete is it?
Names for species are 100% complete, infraspecific taxa (var. and formae) are probably 80-90% complete. The numbers of species are currently for larger groups about 5-10 % higher than the final species count will be, since some provisionally listed species will turn out to be synonyms. 

Is it continuing to grow and if so, how?
Yes, the coverage does grow. New taxa are regularly imported from IPNI. Local checklists, floras and treatments are added once they are available.

Are there any interesting areas of taxonomic contention within your group?
In World Ferns one major area of uncertainty are the many taxa and names described during the last decades in China with uncertain taxonomic status. China is one of the most species-rich areas in the world. The new Flora of China (two of three volumes just published) does a good job for some groups but there are still large groups with plenty of uncertain names to be clarified.

Do you have a favourite species or group of taxa?
Not really. Since I still do entomological work, the most interesting groups are plants who serve as food plants for certain insects (for example Legumes). The evolutionary aspects of this are quite interesting (how does a monophagous relationship between insect and plant evolve? Is it good or bad for the insect?).

Do you have any fun or unusual names in your group?
A recently separated fern genus, Gaga, has been named after Lady Gaga. (The fun is that "gaga" means crazy in colloquial German. I am not sure how many English speakers actually know it.). This created a lot of publicity for an otherwise quite average and unremarkable fern group - good for taxonomy!

What interested you in taxonomy?
Being a Chemist by training, I have been involved in collecting insects, photographing plants and especially doing nature conservation work since my childhood and now for 35 years. Taxonomy and a proper dataset as well as good faunas and floras are the basis for everything to work with. If you try to do thorough work in any group, you are desperately in need of good checklists.

Do you think traditional taxonomy has a future?
Absolutely. Even with very good PCR and genetic results there always needs to be a proper dataset to cross-check the genetic results. With better computers and faster genetic testing, the taxonomic databases will increase in importance.

What is the most exciting recent taxonomic development in your group (if any)?
The Ferns, being a very uniform group with similar morphology and therefore obscured relationships, have for many decades "resisted" to yield a proper taxonomic tree, and many competing classifications were available. Finally, two groundbreaking papers (Christenhusz et al. 2011 as well as Rothfels et al. 2012) provided a reasonably stable framework for the taxonomic tree of the ferns - remarkably much later than similar efforts for the flowering plants.

On the floristic and regional side, there have been two extremely helpful developments: The Ferns of Taiwan (by Ralf Knapp 2010 and 2013) did a remarkable job in clarifying the taxonomy and distribution of the Taiwanese species, which are in the midst of the above described hotspot of East Asian diversity. Now at least, for about 800 species (of 2500 in the region) we have a thorough treatment. Also, Christopher Fraser-Jenkins published a series of carefully researched books about the southern Himalayan and Indian Ferns, where there is comparable diversity to China, and also clarified whole multitudes of names in an area which prior to his work had very messed-up taxonomy.

If you had the funds what improvements (if any) would you make to the database?
Not the funds, but the time and better accessibility of a large scientific library - then a more thorough cross-checking of smaller and midsize papers of genera and groups would be much desirable.

Why did you submit to the Catalogue of Life?
Because ownership of data is respected by the Catalogue of Life and proper credits are given.

Do you submit to any other biodiversity aggregators than the Catalogue of Life?
No, and not planned.

Catalogue of Life wants to thank Michael Hassler for completing our questionnaire.World Ferns checklist was published in the August edition of the Catalogue of Life and the first batch of his plant family checklists (World Plants) will be included in the September release.

Thursday, 22 August 2013

i4Life Part 2: Global Species Databases

GSDs in the i4Life dataflow

Previous posts in this series:
Part 1: Improving the world's taxonomic data indexing

Global Species Databases are central to the success and quality of the Catalogue of Life as they form the core knowledge upon which it is built. As a corollary, they are an integral part of the workings of the i4Life project and the first stop in our data flow blog series (see introductory post). There are currently around 130 contributing Global Species Databases in the Catalogue of Life. But what is a Global Species Database and how do they come about?

A Global Species Database is quite simply a Catalogue of Life term to describe a global species checklist that is in a database. The database software used is not significant (although can help) but the content and the way that content has been structured to support the essential parts of a taxonomic checklist and supply the Catalogue of Life is. In the context of the Catalogue of Life, a global species checklist is a list of all known names worldwide with an associated taxonomic concept (ie accepted name or synonym). They are usually produced by taxonomists although those taxonomists do not necessarily need to be working with primary data (ie specimens). Creating a checklist can be achieved through pulling together published names and concepts from elsewhere (ie existing taxonomic publications, floras and faunas or existing regional checklists) and producing a single authoritative global view for a particular taxonomic group. Once a database is recommended to the Catalogue of Life by independent peer reviewers and accepted by the Catalogue of Life editors, the taxonomist's view is not questioned or altered. However, the structure and consistency of the data needs to be checked to ensure it meets certain data standards for inclusion in the Catalogue of Life. To enable the Catalogue of Life to do this, the submitted checklist is required to be in the form of a Standard Dataset.  On receipt of the checklist in this format, it is then easier for the Catalogue of Life to run a series of quality control checks to query the database's integrity and suitability for inclusion.

The taxon and its underlying taxa does not have to be at any particular rank in the classification. So for example, it could be a global species checklist for one particular genus or family or order, or at any taxonomic rank.

The Catalogue of Life is often criticised for presenting 'one view' of a taxon. Where a decision on classification and species name is from one taxonomic hypothesis rather than presenting the view of two or perhaps multiple. The Catalogue of Life does this purposely for simplicity, as the majority of our users are not taxonomists so do not have the expertise to decide which view to use. However, if more than one is available, the Catalogue of Life will always choose the checklist that it feels offers the most, where conditions such as checklist stability, taxonomist's credentials and global coverage are all considered. If another checklist is submitted that is considered better for our users by reviewers, then it will replace the existing checklist or part of that checklist. For example, imagine the Catalogue of Life accepts a checklist that covers three families with only 85% global coverage of taxa in each. If a new checklist is submitted for just one of those families that has 100% coverage and is judged to be authoritative and meets data standards, it will replace the original checklist for that family.  Existing gaps in the Catalogue of Life are the biggest problem for its users so it tries to achieve as much coverage as possible without compromising quality, but that does not mean that once a checklist is accepted it no longer reviews the quality of the names it holds over time.

Why do taxonomists contribute their global species checklists to the Catalogue of Life? The Catalogue of Life acts like a shop window for Global Species Databases, promoting them through the website and Annual DVD publication, as well as outreach activities around the world; whilst always ensuring that they receive full credit for their work. There is still no stable inventory of all known species, but Global Species Databases in partnership with the Catalogue of Life have done more than any other initiative towards achieving this goal, creating a unique taxonomic resource in the process.

Next up: i4Life Part 3 The Catalogue of Life

Tuesday, 20 August 2013

The European Marine Biology Symposium, Galway, Ireland, 19-23/08/2013

Thomas Kunze, Viktor Didzulis and Yuri Roskov attended the European Marine Biology Symposium, Galway, Ireland, 19-23/08/2013 and offered three posters on the progress of the i4Life project.

Monday, 19 August 2013

Taxon of the Day: Dracaena draco

Dragon tree

Taxon of the Day looks at another species assessed as vulnerable by the Catalogue of Life's partner organisation the IUCN Redlist: Dracaena draco (L.) L. is commonly known as Dragon tree or just Draco and is native to Macronesia and Morocco including the island of La Palma where this photo was taken. Seen in the wild, a mature specimen is a spectacular sight however not so much when seen, as is common in temperate climates, as a houseplant - popular mostly due to its toughness rather than its beauty in a pot. Similar to a previous Taxon of the Day entry Yucca brevifolia, it has the word tree in its common name, yet it is highly questionable whether it would be wise to categorise it as such. A monocot in the plant family Asparagaceae it has some characteristics which may make us think tree! Most noteably it looks like one, with a tree-like growth habit. Starting with a single stem that branches, that offshoot then grows for about 10-15 years before re-branching itself, finally resulting in the umbrella like configuration shown in the photo. However, unlike a conventional tree, it doesn't have growth rings so age is calculated by counting branching points. The oldest known specimen, currently found on Tenerife, is thought to be around 250 years old. It also has no use as a timber product but its red resin (Dragon's blood) has historically been used as a dye, including as a stain for Stradivarius violins.

It has been well represented in culture and mythology appearing most noteably in the fantastical triptych The Garden of Earthly Delights painted by Heironymous Bosch (the featuring section is shown below) and in the Greek myth The Apples of The HespĂ©rides. It also acted as a backdrop to Marylin Monroe in Some Like It Hot, where the tree (or plant) in question continues to be a tourist attraction outside the Hotel Del in San Diego, California.

The Garden of Earthly Delights

CoL Annual Checklist: Dracaena draco (L.) L.
CoL contributor: World Checklist of Selected Plant Families
Image copyright: Zyance [CC-BY-SA-2.5], via Wikimedia Commons

Friday, 16 August 2013

Taxon of the Day: Culicidae

Aedes aegypti
Feeding mosquito

Taxon of the Day is back after a short break. During that break TotD was inspired to write a post on today's subject which went by the local name of Komarci (pronounced Kamartze or more frequently argh Kamartzeee!). Back home in the UK they go by the name mosquito from the spanish mosqua meaning fly and the diminutive suffix -ito meaning little and constitute a large group (over 3,500 so far described worldwide) of insects in the family Culicidae.

We are extremely lucky here in the UK, where the Catalogue of Life is based, that today (although not so historically) mosquitoes are a nuisance rather than life-threatening, and whereas in other parts of the world we know they transmit diseases such as malaria, yellow fever, dengue fever and more, we just have the biting, swelling and itching to contend with.  There are a little over 30 different reported species in the UK, a full list of which can be found on the Public Health England website. A quarter of these do not bite humans, preferring animals and birds instead. There have been five reported non-native species in the UK although not for many years. A species that causes some concern is the Asian tiger mosquito (it has stripey legs!)  Aedes albopictus, which transmits West Nile virus, yellow and dengue fever but not malaria. Perhaps because it is as close as Belgium a number of mis-identifications have occurred in the UK, which later have all been confirmed to be the species Culiseta annulata, a common and widespread mosquito of the British Isles. The Department of Health believes the likelihood of transmission of disease via mosquitoes in the UK remains low although some indicators have suggested increasing numbers in recent years. It is believed that British mosquitoes will be affected by climate change, if they haven't been already, with higher temperatures and extreme weather providing new habitats for mosquitoes to breed.

CoL Annual Checklist: Culicidae
CoL contributor: Systema Dipterorum
Image copyright: Danny Steaven [CC-BY-SA-2.0], via Wikimedia Commons

Thursday, 15 August 2013

Catalogue of Life in the Azores

Thomas Kunze with his poster

Outreach is important to the Catalogue of Life firstly, to disseminate the work that we do to the scientific community and the general public and secondly, as a way to seek out taxonomists working in our gap areas. Eventually we hope to complete our list of all known species on earth but to do that we need to attract more contributors. Part of this outreach activity is attendance at relevant scientific conferences. Last month Thomas Kunze attended The World Congress of Malacology. Below is an account of his trip: 

The World Congress of Malacology is the largest meeting of malacologists and is held every three years around the world. Malacologists are those people working with molluscs, a phylum of invertebrate animals including significantly gastropods (e.g. snails and slugs), bivalves and cephalopods (cuttlefish, octopus and squid). After Phuket 2010 the congress was this year in Punta Delgada on San Miguel the largest island of the Azores. The Azores are a Portuguese island group in the middle of the Atlantic and are also inhabited by diverse land snails. 

With almost 400 participants a good number of mollusc specialists attended this year. Beside specialists and well known researchers, there were many students attending the meeting. It is always a great occasion to meet colleagues, listen to groundbreaking talks and chat over the study object: molluscs. In previous editions the Catalogue of Life (CoL) listed only 14,277 molluscan species but in recent months the CoL editorial team has merged several (regional and global) checklists for gastropods and bivalves, and now the CoL includes a large checklist of molluscs with 41,655 species. Of course these results had to be presented on the Azores! 

Besides presenting data to the worldwide community of specialists, a conference like this helps not only to exchange new ideas and views but also to search for contributors to the CoL. Although the CoL now has a large checklist of molluscs from marine and freshwater habitats, there is not a checklist for terrestrial gastropods, which 
with around 20,000 to 30,000 species constitute the biggest remaining gap in molluscs. So the WCM is a platform for searching out new partners who can provide terrestrial snails and slugs to the CoL.

Thursday, 8 August 2013

i4Life Part 1: Improving the world's taxonomic data indexing

The i4Life project is enabling a flow of names and taxonomic concepts between the Catalogue of Life, its supporting Global Species Databases and the internationally used biodiversity data portals.

What this means is whether you are looking for DNA sequences, distribution patterns or conservation status of your chosen species, the shared and interlinked catalogues of organism names in i4Life will help you to find the same plant, animal, fungus or micro-organism under the same name in each data portal.

How is it doing this?  Well it is utilising a number of informatics tools developed during the lifespan of the project to manage both the cycle of taxonomic data flow between data providers and the processes that enable taxonomic improvements along the way. This system, and the high level of collaboration that is required among project partners to make it work, is depicted in the i4Life workflow diagram below. Over the coming weeks on the blog, we will look at some of these tools in detail to see what exactly they are doing and how they are doing it. In the meantime please see if from the diagram you are able to work it out yourselves!

The i4Life system diagram
Next up: i4Life Part 2: Catalogue of Life

Monday, 5 August 2013

Taxon of the Day: Poaceae

Bromus hordeaceus hordeaceus

Today's Taxon of the Day has been produced by Dr M, he writes:

Poaceae is a wonderful and important vascular plant family, the 5th-largest in the world, after Orchidaceae, Asteraceae, Fabaceae and Rubiaceae. Catalogue of Life lists 740 genera and 11,367 species. Poaceae is important ecologically, economically and aesthetically:

Ecologically natural and semi-natural grasslands cover 20% of the Earth but Poaceae occur in many other habitats too like forests, freshwater and saline wetlands and tundra. Fascinating ecological relationships have evolved including the co-evolution between grasses and large grazing animals and between grasses and wildfire.

Economically the early domestication of Poaceous cereal crops e.g. maize, wheat, barley, millet, and rice laid the foundations for human societies around the world. Even today Poaceae is the most economically important plant family, providing forage, building materials, fuel as well as staple food crops.

Aesthetically grasses must count amongst the most evocative and beautiful plants on Earth. We only have to think of the mysterious swirling Stipa grasses on the Steppes of Eastern Europe and Central Asia, the herds of Antelope, Wildebeest, Buffalo and Zebra migrating majestically across the Savannas of East Africa, and even fields of cultivated wheat and rice have their own Poaceous magic. Not only a Taxon of the day but a taxon for all time!

Further reading and sources:

RBG Kew - GrassBase http://www.kew.org/data/grassbase/
Watson & Dallwitz - Grass Genera of the World http://delta-intkey.com/grass/
Clayton & Renvoize - Genera Graminum http://www.kew.org/science-research-data/directory/projects/GeneraGraminumEd2.htm

CoL Annual Checklist: Poaceae
CoL contributor:  World Checklist of Selected Plant Families
Image copyright: Dr M

Thursday, 1 August 2013

Taxon of the Day: Acinonyx jubatus

Acinonyx jubatus

Today’s Taxon of the Day has been produced by Thomas Kunze, he writes:

Acinonyx jubatus (Schreber, 1775) or cheetah is the absolute sprinter beyond all land animals. Being the fastest one on land it can speed up to 64 mph (Sharp in Journal of Zoology 1997) and then hold its speed for a maximum of 400 m. Recent research has shown that the cheetah does not reach its top speed very often but instead uses its power and ability to manoeuvre while hunting its prey (Wilson et al. in Nature 2013). Besides its slim body, long narrow legs and wide nose channel it is the claws that are especially adapted to its high speed. The claws are not completely retractable like in most other cats and work like spikes on running shoes in order to give more grip to the cat. It is also referenced in the scientific genus name Acinonyx coming from the Greek meaning “immobile –claw”.

The pictures of the cheetahs in this post were taken in the Amboseli National Park in southern Kenya. Two of them were lying in quite high grass next to some shrubs (see below) and were very well hidden by vegetation and their colour patterns. Adult females are solitary whereas adult male brothers live and hunt together. When a group of zebras passed close by they got a little bit more excited and rose. This was when the picture above was taken. The black tear shaped eye marks are very visible.

Spot the cheetahs!
The genetic variation within cheetahs is exceptionally low and has likely been caused by a bottle neck event around 10,000 years ago. Most of the cheetahs live in Africa. However, there is a small, highly endangered population of the Asian cheetah in Iran, Acinonyx jubatus ssp. venaticus (Griffith, 1821). This subspecies is listed as critically endangered by the IUCN Red List and Acinonyx jubatus is recorded as vulnerable.

CoL Annual Checklist: Acinonyx jubatus
CoL contributor: ITIS Global
Image copyright: Thomas Kunze