We chat with ichthyologist John P. Sullivan about his new research portal for African freshwater fishes.
John is Curatorial Affiliate at the Cornell University Museum of Vertebrates, Ithaca, New York, USA, and Research Associate at the Academy of Natural Sciences, Philadelphia, USA. He has conducted extensive fieldwork in several African countries and published numerous scientific papers with a particular focus on ichthyology, phylogenetic systematics and taxonomy of African electric fishes (Mormyridae) and catfishes (Siluriformes).
Alongside Dr. John Friel of Cornell University he has developed a new online resource which launched recently, and SF caught up with him this week to find out more.
What is Africhthy?
Africhthy (http://africhthy.org) is a website for African ichthyology that we’ve only just launched and to which we are rapidly adding users and content. We hope it becomes a place where professionals and amateur ichthyologists alike can go to find literature, images, keys, and expertise on African fishes, and to find collaborators for projects and research.
How did you get involved and who else is working on the project? Why Africa?
Dr. John Friel is curator of fishes at the Cornell University Museum of Vertebrates, and he and I have been studying African freshwater fishes since the late ’90s (he mostly mochokid catfishes and I mostly mormyrids). Between the two of us, we’ve traveled to quite a few different African countries for fieldwork. The idea for Africhthy grew out of our experiences in Africa and our interactions with our African, European, and North American colleagues.
We were both struck by the fact that most of the countries we’ve visited lack the institutional capacity to identify their own fishes. Often when we would bring the literature needed to key out fish specimens, it would be the first time that anybody in those countries had seen it. At the 2008 Pan African Fish and Fisheries meeting in Addis Abeba, it was clear that many African ichthyologists who gave presentations on their research were using taxonomies that were decades out of date because they lacked access to recent literature.
Science is about communication and building upon what’s already known. Without access to recent (as well as classic) scientific publications and other kinds of data, African ichthyologists are effectively unable to contribute to knowledge of their own fish fauna to the rest of the world. With dam building and other kinds of development impacting freshwater ecosystems across Africa like never before, it’s imperative that we develop real expertise in ichthyology *in* Africa. During our visits, our African colleagues would frequently ask us for our entire pdf libraries. It occurred to us it would be far more efficient to consolidate information on African fishes on a website like this, for everyone’s benefit, (including our own). Projects like the Biodiversity Heritage Library are making most of the old literature available online and some science publishers that aren’t generally open access do offer free access from IP addresses originating from developing countries. What’s needed is an updated taxonomy of African fishes linked to a comprehensive bibliography with pdfs downloadable from the site, or from links on other sites, as well as to online data sources like GenBank, GBIF, Wikipedia, the Encyclopedia of Life and FishBase. We’re building Africhthy in order to provide this. Of course, it’s not as though only people in developing countries will benefit from a site like this: all of us will.
At the same time, we noticed that gathering dust on the bookshelves of government agencies, conservation NGOs and universities in these countries is a lot of information on freshwater fishes (and other organisms) that few have ever seen: unpublished “gray” literature. Commonly these are unpublished faunal surveys and studies of the feeding ecology and reproductive ecology of African fishes. These sources aren’t peer-reviewed and their quality runs the gamut, but much of it would be very useful were it scanned into pdf format, linked to key words, and made available online. Knowing where faunal surveys have already taken place is crucial for preventing duplication of effort and for those trying to make informed policy and conservation decisions. Users can upload and index documents up to 30 MB in size on the Africhthy site and protect their copyright with a Creative Commons license. Everything that gets uploaded to Africhthy can be associated with pull-down lists of taxonomic and geographic search terms from updatable taxonomies so that if names change in the future, the link remains. We hope Africhthy becomes an archive for this kind of gray literature on African fishes.
While the internet is not as ubiquitous a presence in the lives of most Africans as it is for those of us in the developed world, it is increasingly available. All college students in D.R. Congo, for example, poor as most are, have a laptop that enables them to access the internet when possible from a university connection or a cybercafé in town. For these students time is of the essence when connected. They often pay by the minute for their connections and so there is no time for idle surfing. A single site where one can quickly locate literature and read recent studies on African fishes would be really useful to them.
So, access to literature, both the published and the gray kind, and aggregation of data on African fish species located elsewhere on the web is a big part of what Africhthy is about. Another is getting access to each other. Africhthy is intended to be a kind of social club. We need a way to find colleagues with similar interests in order to share information and to collaborate. For instance, I’d really like to find a research partner in the new country of South Sudan interested in the mormyrid fishes of the White Nile. Perhaps there’s a South Sudanese student or researcher out there looking for someone like me, but how would we ever find each other? The answer may be a website like Africhthy. We’re hoping that people use the forums and bulletin boards to let others know their research interests and seek out collaborators as well as to broadcast requests for specimens, photos, tissues, etc. Of course, we have to get the word out about the existence of Africhthy to places like South Sudan and we’ve barely begun to do that.
Who is the resource aimed at and who is able to access it?
It’s open to everybody. While Africhthy is somewhat aimed at African ichthyologists, we think it will be equally useful to everyone who’s interested in African fishes, wherever they come from, and whether their involvement is in a professional capacity, or as a hobbyist. To add content to the site and have access to its full functionality, you need to register. As I write this we have 67 registered users, many of them African. Hopefully we can crest 100 before long. One important aspect of the site is that it is bilingual, English and French. These are the two most widely spoken European languages in Africa. While John Friel and I are both native English speakers, we are making an effort to get as much of the interface translated into French as well as English. At this stage, we really need people to register on the site and contribute content: bibiographic references, images, forum posts and blog articles (in English or French).
The Scratchpad web format is unfamiliar, can you explain a little about it and why it was chosen?
Scratchpads http://scratchpads.eu are part of the E.U.-funded ViBRANT project (http://vbrant.eu) and are based at the Natural History Museum in London. Scratchpads are remotely hosted, Drupal-based, customizable web environments that enable communities of taxonomists and other biologists to share, manage and publish data on the web. Currently there are 311 Scratchpad sites created for all variety of plant and animal taxa as well as for online journals and societies and over 6000 registered users. (See the list of sites here http://scratchpads.eu/scratchpads/thumbs) They are free to create, and after learning about them, the usefulness of creating one for African ichthyology was clear to us. Given the level of participation in the Scratchpads project, it seems likely the E.U. will continue committing resources to the Scratchpads project into the future. Africhthy is currently still in version 1 of Scratchpads, but version 2 is in development and promises a much slicker appearance with enhanced features. You can see a test version of the next-generation Africhthy site at http://test-africhthy.myspecies.info/. Africhthy will probably be ported to version 2 in the near future.
How do you envisage the site moving forwards?
I am hoping to be surprised by the evolution of Africhthy. The directions in which it goes and which functions become the dominant ones will be determined by those who use it. While I think it will remain largely a literature archive and fish identification tool, I am hoping it may become popular as a blogging platform, a discussion forum, or eventually even a publishing platform. Version 2 of Scratchpads will at some point have a module allowing one to submit a species description directly to the Pensoft journal Zookeys. We welcome interested readers of Seriously Fish to check out Africhthy, register accounts and help us build it. We’re hoping it catches on and that Africhthy becomes a model for how to organize and create a cyber-infrastructure for an international biodiversity community.