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BITC / Biodiversity Diagnoses - Basic Patterns 1

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Good morning everybody, today what we're going do is to get a bit deeper into this idea of inventories and some of the statistics that accompany them. And begin exploring these ideas of completeness, gaps, and other related things. So first of all, I'll just give you a bit of an overview just some basic thinking about assembling inventories and specifically this idea of regional diagnosis. And so we can take as a goal, "providing a comprehensive view of the distribution and diversity of a major taxon across a country or region." So some area of interest, some taxon that is diverse enough to be of importance and some region that is diverse enough to be more than a single site. And essentially all I want to do in this talk is to lay out for you some sources of this information. Because really as Arturo mentioned, time is unidirectional and so either the information exist or not. And particularly if you want a view of your region and your taxon that goes back far enough that it can include historical information, either the information exist or it doesn't. So centrally we can explore four broad categories of sources of information. 1. We can work directly with old specimens in museums in some cases new specimens in museums 2. We can use online data sources such as GBIF, Vetnet, SANBI, species link, and download data. 3. With Rodrigue's project, we saw De novo data collection. And 4. One little I will throw in out of interest is the idea of existing monographs. Dorothy, Moses and I were talking about this last night a bit. So I just want to give you a broad overview of this idea and give you some examples of these four approaches. And then as we talk about yesterday coding controls everything. Either you have the coding control done well or you fall into garbage-in-garbage-out. So kind of the ultimate in terms of documentation of biodiversity is specimens. And the beauty of specimens is, you can go back to them, check them and reinterpret them. And they can be frustrating in that you'll get old data labels like this that really don't have much information on them. But if you considered that that might have been about 150 years agro, maybe that's pretty impressive. You know I always forget when I'm looking at older specimens, sometimes those specimens predict Darwin, or at least Darwin's publication of the 'Origin of Species'. It's not all uncommon to be working in the bird world with specimens from the 1850s. But this is just some illustrations of bird some specimens, kind of closed up to give you an idea of what our labels look like. It's not as bad as insects speciemens, but we'll frequently have a couple of different labels tied to a specimen. And there are all sorts of customs and formalitity about what kind of labels get put on what kind of specimens, how they're writen. This is a collection in Los Angeles and I found that picture on the web. A colleague of mine John MacCormick and the group that both of us did our dissertations on which the New World Jays. And then this picture is just spectacular this the US National Museum collection (the Smithsonian collection). And this woman was Roxie Laybourne, she was a forensic ornithologist. So her job was to identify bird parts (usually feathers) from anywhere (usually from criminal investigations). And back when she was working it was not just the specimens out in the collection, which is about 85-90% of the bird species on earth but also her own personal files of feathers from thousands of birds. So they took this picture when they opened every drawer in the lower tier of the cabins in the collection and that's an amazing collection. So this really is the ultimate documentation. And the neat thing about specimens is you can even go back as species concepts changed, you can perhaps do DNA sequecing, and get the full and proper identification. Whereas even the very best in my world bird watcher can say oh yes I had such and such of species, and you say oh now we recognise two species out of that one. Which one was it? So this really the ultimate documentation. And I want to give the idea of the depth fit you get, this the 25 years project that I mentioned yesterday the XXXX of the distribution of birds of Mexico. And we started with institutions that would provide us with their data set and then we will (this was back in the 1990s) go to the collection and verify the data set. Then we moved on to a bunch of institutions where we captured their data. In fact, of the 80 plus institutions that are included in this data set, for thirty-two of them we did all of the captured of all of their data. The British Museum which is one of the largest collection in the world with more then a million bird specimens, we computerized 15000 Mexican bird specimens from their collection and last I heard that was their progress in the digital capture data associated with their collection. Maybe they've added something since but for a long time their computer catalogue of their collection was our 15000 records that we captured and gave back to them. So 32 museums in which we did all of the captured and then another 40-50 collections where we either verified or used digital data. But we are now above 400,000 specimens for the country. And you can see there is a pretty amazing density of records. There is still some holes, this the Chihuahuan Desert and the desert of the Bahia Peninsula and some areas in the interior in very remote areas. But really this the data set from which we've derived dozens of publication because it's so rich and comprehensive. So it is very possible to develop these summaries. And so you can do plot through time as Arturo showed you yesterday. And in the case of Mexico, you should notice that the second World War didn't make a difference. Anybody body know what this is? It is the first War World but that's not why Mexico has zero collection records [Participant] that's during the period of the Mexican revolution So Mexico had a kind of feeder systems where there were huge land owners in the 1910s you had a massive popular uprising that basically removed the phrase was "the land belongs to those who work it". Yes, XXXXX. So you see those historical things you can see the accumulation of records through time. And right away we to our first gap, because we're going to be talking about gaps a lot. But you can right away that before 1850 we know almost nothing. In fact, my colleague and I a few years ago got to work on a new data set that had been lost since the 1780s. In the XXXX, the Spanish Royalty sent an expedition in the 1780s and they collected all across Mexico, and sent specimens back, sent paintings back and sent manuscripts back. And the ornithologist came with the collection and developed manuscripts, and then he died. When Napoleon was invading across the continent, the manuscripts got lost. The specimens appeared to have been destroyed but the manuscript was lost and eventually, in 2002 the manuscript was found not in the Archive of the National Museum of Spain, but not the shelf with the books. And so in order to get species accounts for 200 species, that were in this lost manuscript, the terrible thing was that it was written in Latin. And so we had to go back and relearn our Latin from High School. But here's what Mexico looks like. This is the Mexican bird data. This a pretty common reality, there's some small portion that's held in the Mexican collections. You see I have used the color of the Mexican flag obviously. But then three-quarter of the data are held in institutions around the world. So if you want a complete picture of the specimen record of your country, you not only have to work in the national museum or the university collections but you also have to then track down where have all those foreign collections gone to. For here in Africa, you may get a slightly narrower set of possibilities because of colonial heritage. If we are talking about Benin, we know that we have to look principally in France. There're probably Beninese collections elsewhere but we know the biggest one. This is a big challenge to getting a big picture of a taxonomy for a region based on specimens. Which is to say it a highly dispersed and distributed data resource. And projects like Vetnet and GBIF help but if this museum has not gotten the digital capture and sharing of its data, then you're missing 10 percent of the data. So you're very vulnerable to dead institutions, lazy institutions and selfish institutions. And your data depend on people that you don't know and people who might not share the same goal you have. So again I considered specimens to be the ultimate resources, but not necessarily the easiest. And that's not to mention the complications you'll have in harmonizing the data across all of these institutions. For the Mexican project basically two or three of us visited all of the collections and thoroughly checked all of the specimens. Which took a lot of time. So our second resource are monographs. And this an interesting one. Sometimes there exist a very detailed monograph that really compiles the state of knowledge as of some point in time. So I grabbed this monograph mainly because it's open access. As of 1932, the American Museum of Natural History had a very big program in the DRC and this man Chapen directed a lot of the work and assembled this monographed. And I was little bit disappointed in its content because you get things like this, very useful compilation Chapen's understanding of the history and so you know I need to figure out where this set of collections are and this set of collections and this.

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Duration: 16 minutes and 18 seconds
Language: English
License: Dotsub - Standard License
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Posted by: townpeterson on Aug 30, 2016

This talk was presented in the course on National Biodiversity Diagnoses, an advanced course focused on developing summaries of state of knowledge of particular taxa for countries and regions. The workshop was held in Entebbe, Uganda, during 12-17 January 2015. Workshop organized by the Biodiversity Informatics Training Curriculum, with funding from the JRS Biodiversity Foundation.

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