Category Archives: DNA

The Race: GG VII – – First Week: Snakes, Workshops and Spiders

Our first week is now complete. The botanists and Andrew our photographer went to Príncipe early so I will include their progress in a later blog. One thing I will add though is a picture Andrew emailed us yesterday, a shot of the endemic diurnal green snake, the Príncipe Soá-soá. We have only been able to collect one of these (GG I); it is an extremely elusive species.

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Hapsidophrys principis  A. Stanbridge phot. GG VII

Signe Mikulane, a PhD student at the University of Heidelberg had been in contact with me during the past few months and delayed her return to Germany to be with us for a week. She joined us in our early school visits, and especially our annual check of the status of the large tree where we find the Sao Tome giant treefrog.

 GGVII Photos  - 681 V. Schnoll phot. GG VII

 We found no adults but Signe dug her hand into the tree hole and came up with tadpoles, so we know the tree is still in use. In the picture above, there are several tadpoles in her hands.

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  Velma Schnoll &Signe Mikulane return from the frog tree

RCD phot. GG VII

With the arrival of Roberta Ayres (and Dr. Szuts) the biodiversity education team was complete.

P1010209Ayres and Szuts arrive in Sao Tome RCD phot. GG VII

Saturday we held our first ever teacher workshop at Escola Primaria Maria de Jesus, the largest primary school in the country (2,000+ kids).

IMG_2293RCD phot GG VII

 We spoke to 58 teachers about island biodiversity in more depth so that they can use the materials we have brought more efficiently. The hour and a half presentation was extremely well received, even though we had to project our powerpoint on the back of a canvas painting!

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RCD phot GG VII

Although we are concentrating on fourth grade this year, the teachers were from all grades and we have already noticed that our materials, the posters, the coloring books, etc. are used widely at many different levels.

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The education team: Velma Schnoll, Roberta Ayres, Roberta dos Santos

RCD phot GG VII

Dr. Tamas Szuts, Professor of Biology at the University of West Hungary is our jumping spider expert. We took him into the field early, to the south end of the island and he began collecting.

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Here, Tamas is using a simple sweep net. RCD phot GG VII

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Tamas is using a beating pan here. He holds it beneath a bush and beats the latter.  RCD phot GG VII

 By the way, these pictures do not do Tamas justice. He is about 6’ 8” tall. He brings specimens back live and then photographs them in great detail.

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 This is Tamas photo setup in our room and the results are truly spectacular RCD phot GG VII

By the way, the bottle on the right is NOT vodka; it is lab grade ethyl alcohol for the preservation of DNA,

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T. Szuts photos GG VII

The second two images are salticid, or jumping spiders; the first is of a different group.

In this YouTube video, Tamas Szuts describes his fieldwork: http://youtu.be/LDdFMn0eARw

More soon when Rayna, our frog student arrives and we reunite with the rest of the science team.

Here’s the parting shot:

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Satocao workers returning from cacao plantation V. Schnoll phot GG VII

PARTNERS:

We are most grateful to Arlindo de Ceita Carvalho, Director General, Victor Bomfim, and Salvador Sousa Pontes of the Ministry of Environment, Republic of São Tomé and Príncipe for their continuing authorization to collect and export specimens for study, and to Ned Seligman, Roberta dos Santos and Quintino Quade of STePUP of Sao Tome http://www.stepup.st/, our “home away from home”. We gratefully acknowledge the support of the G. Lindsay Field Research Fund, Hagey Research Venture Fund of the California Academy of Sciences for largely funding our initial two expeditions (GG I, II). The Société de Conservation et Développement (SCD) and Africa’s Eden provided logistics, ground transportation and lodging (GG III-V), and special thanks for the generosity of private individuals who made the GG III-V expeditions possible: George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor, Velma and Michael Schnoll, and Sheila Farr Nielsen; GG VI supporters include Bom Bom Island and the Omali Lodge for logistics and lodging, The Herbst Foundation, The “Blackhawk Gang,” the Docent Council of the California Academy of Sciences in honor of Kathleen Lilienthal, Bernard S. Schulte, Corinne W. Abel, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. John Sears, John S. Livermore and Elton Welke. GG VII has been funded by a very generous grant from The William K. Bowes Jr. Foundation, and substantial donations from Mrs. W.H.V.“D.A.” Brooke, Thomas B. Livermore, Rod C. M. Hall, Timothy M. Muller, Prof. and Mrs. Evan C. Evans, Mr. and Mrs. John L. Sullivan Jr., Clarence G. Donahue, Mr. and Mrs. John Sears, and a heartening number of “Coolies”, “Blackhawk Gang” returnees and members of the Academy Docent Council. Once again we are deeply grateful for the continued support of the Omali Lodge (São Tomé) and Bom Bom Island (Príncipe) for both logistics and lodging and especially for sponsoring part our education efforts for GG VII.

Our expeditions can be supported by tax-deductable donations to “California Academy of Sciences Gulf of Guinea Fund”

The Race: Island Biologists in Training

Jens Vindum, Senior Collections Manager, Department of Herpetology. (phot D. Lin-GG I)

I need to add and addendum to last month’s blog, “Why We collect Specimens.” Our Senior Collections Manager, Jens Vindum (GG I, GG II) has just informed me that since 2003, there have been 33 international scientific papers published on our Gulf of Guinea reptile and amphibian specimens and/or tissue samples from them!

Clearly, the scientific world is beginning to hear about Sâo Tomé and Príncipe! At this point, I do not know how much of our material from other disciplines has been used but certainly our samples are in labs all over the world.

We have been extremely fortunate to have been able to bring a series of our graduate students with us on a number of our expeditions.  Not only have most flourished academically and many have published on their island projects, they represent a cadre of new young scientists who have an understanding of the uniqueness of the islands and the people who live on them.  All have interacted closely with local island citizens and as a result, function as young biology ambassadors for these fabulous islands.  Overall, the islands are still very poorly known to the outside world, but we are getting there!  Here are our young colleagues:


Lindsay Wilson on Bioko Island with bush viper.  RCD phot – 1998

Lindsay Wilson was a participant on our 1998 expedition to Bioko, the first island in the Gulf of Guinea chain. She completed her MSc on African treefrogs of the genus Hyperolius at San Francisco State University with highest honors.


Joel Ledford on Sao Tome.  D. Lin phot- GG I

Joel Ledford joined Gulf of Guinea I as the graduate student of Dr. Charles Griswold. He completed his MSc at San Francisco State and then his PhD in spider systematics at the University of California, Berkeley.


D. Lin phot – GG I

Also on GG I was Ricka Stoelting, my graduate student. She completed her MSC on the endemic caecilian of Sao Tome (she is holding one, above) and is currently a PhD candidate at the University of Wisconsin.  She is also working on the publication of her MSc work at San Francisco State (SFSU).


B. Van Syoc photo – GG III

Dana Carrison-Stone was a participant of the marine expedition, GG III as the graduate student of Dr. Bob Van Syoc.  Dana discovered two new species of barnacles from the islands and they are part of her MSc which she completed last year at SFSU.


D. Lin phot – GG II

Josef Uyeda was on GG II and again GG on III as an undergraduate at Willamette University and one of my Summer Systematics interns.  During his island work, he discovered and described a new species of frog from Sâo Tomé. As I write, he is defending his doctoral thesis (tomorrow!) at Oregon State University. Flash!! Josef finished his PhD today! (Oct 5)

 

                                                                                                             unknown phot.

Mac Campbell, also a Willamette undergrad, joined GG II as an assistant to our ichthyologist, Dr. Tomio Iwamoto.  He has since completed his MSc at University of Alaska, Fairbanks and is currently a PhD candidate in fish systematic at the same institution.


Weckerphoto – GG III

Rebecca Wenk joined GG III as the grad student of Dr. Tom Daniel one of our senior botanists.  Rebecca’s work resulted in her successful completion of her MSc at SFSU and also an excellent scientific publication on plants of the family Acanthaceae.  Tragically, Rebecca died of a serious illness last year.


A. Stanbridge phot – GG IV

Miko Nadel is a graduate student at San Francisco State, studying under Dr. Dennis Desjardin, the mycologist on GG II and GG III). Miko was a participant on GG VI doing the first comprehensive survey of lichens on the island.

A. Stanbridge phot. GG VI

Rayna Bell also joined us on GG VI, studying color variation in African treefrogs. Rayna is a PhD candidate at Cornell University.

The people above were or still are graduate students who have actually worked on the islands with us.  But they are not the only young academics studying our Gulf of Guinea Island material.  Here at the California Academy of Sciences we have a program known as the Summer Systematics Institute (SSI). This program is funded by the National Science Foundation, and undergraduate students can apply to work on scientific projects for the summer under the mentorship of a CAS faculty member. Here are those that have worked on Gulf of Guinea specimens. I have not included students who started as undergrad SSI interns and later became our grad students (Lindsay Wilson, Josef Uyeda and Ricka Stoelting).


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Katie Marshall was an Occidental College undergrad and my SSI intern in 2006.  Katie studied the genetics of the Oceanic treefrog, Hyperolius molleri, the only Gulf of Guinea endemic frog that occurs on both islands.  Katie is currently a PhD candidate at the University of Washington, studying the genomics of marine bacteria.

RCD phot.

Lisette Arellano was an undergrad at the University of California, Santa Barbara when she joined us as my SSI intern in 2009. Lisette examined the morphology and genetics of cobra jita snakes (Lamprophis), long thought to be the same species on Sâo Tomé and Príncipe.  Lisette showed that in fact the two island populations are genetically quite different, also recognizable by color pattern as distinct.  Although we know each island is a different species, we have been unable to publish new names because the relationships of the same group on mainland Africa are still very unclear. Lisette is currently a PhD candidate in Biology at the University of Colorado.


RCD phot – 2010

One of the last vertebrates one would predict to be native to an oceanic island is a shrew, largely due to physiological constraints. During the SSI summer of 2010, Eden Maloney’s DNA work showed that the Sâo Tomé shrew, Crocidura thomensis, did arrive on the island naturally, probably many thousands of years ago and is a true endemic species. Its nearest relative is a different species found in eastern South Africa.  Eden has just graduated from the University of California, Los Angeles and is applying to graduate schools.  We are working on publishing her work.

unkown phot.

Lizzie Miller of the University of California, San Diego was my most recent SSI intern (2010). Lizzie has graduated and is now in graduate school at UCSD studying fish systematics.  Readers will already know from this blog that Lizzie discovered and described a new species of gecko from Príncipe, Hemidactylus principensis.

Lauren in Nigeria. D Blackburn phot – 2012.

Lauren Scheinberg is also a grad student at San Francisco State University. Although never an SSI intern nor has she been with us to the islands, she was my lab assistant on a long-term physiology project and now works as a curatorial assistant in our department.  She has become involved in a rather complicated taxonomic problem with the island skinks of the genus Afroablepharis. Like Lisette’s snakes, we know from the work of colleagues in Madeira and Portugal that the skinks are different species on Sâo Tomé and Príncipe.  Unfortunately, material we loaned them that formed part of the basis of this hypothesis was somehow lost in transit.  Lauren has analyzed our remaining material but collating the information generated by different labs can be extremely difficult.  But we are working on it.

Plans are already afoot for GG VII next year.

Here’s the parting shot:

Joy on the way to Rolas, Sao Tome.. B. Simison phot. – GG VI

PARTNERS
We gratefully acknowledge the support of the G. Lindsay Field Research Fund, Hagey Research Venture Fund of the California Academy of Sciences, (GG I, II), the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging (GG III-V), STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bomfim, and Salvador Sousa Pontes of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to collect and export specimens for study. Special thanks for the generosity of private individuals who made the GG III-V expeditions possible: George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor, Velma and Michael Schnoll, and Sheila Farr Nielsen; GG VI supporters include HBD of Bom Bom and the Omali Lodge for logistics and lodging, The Herbst Foundation, The “Blackhawk Gang,” the Docent Council of the California Academy of Sciences in honor of Kathleen Lilienthal, Bernard S. Schulte, Corinne W. Abell, Prof. & Mrs. Evan C. Evans III, John and Judy Sears, John S. Livermore and Elton Welke.
Our expeditions can be supported by tax-deductable donations to  “California Academy of Sciences Gulf of Guinea Fund”

The Race: Why We Collect Specimens!

Summer has been extremely busy.   Our irrepressible bryologist, Jim Shevock, comes into my lab almost weekly with new moss discoveries from GG VI.  He says a new paper on Fissidens (the largest moss genus on Sâo Tomé and Príncipe) is almost finished and will be submitted for publication as soon as he and his colleagues (from the US, the Netherlands and Lisbon) complete a key to identification of the species. Recall that Jim nearly doubled the number of collections he made during GG IV… He thought he had seen everything! The mesa on Príncipe will be a primary target for our botanists on GG VII, next year (see below).

 

Phrynobatrachus leveleve – RCD phot, GG VI

A nice surprise from GG VI was that we finally got some nice, un-posed  photographs of the Sâo Tomé puddle frog, Phrynobatrachus leveleve. Readers may recall that we described this new endemic species back in 2007 following GG II (leve leve means “take it easy” in the local language).  Obviously the way to get good shots of these critters is at night!

Ptychadena newtoni.  A. Stanbridge phot – GG VI

Another good find on a different night was Newton’s rocket frog (Ptychadena newtoni) at a new locality, Caxueira.

The creek at Caxueira.    A. Stanbridge phot. – GG VI

In earlier days I was concerned that this species, endemic to Sâo Tomé, was on the wane due to human development, but it appears to be more widely distributed than we thought (see also Feb 2011 blog). Caxueira is not far from the city center.

Why do we collect plant and animal specimens? Why do we bring them home euthanized and preserved (or in the case of plants, pressed and dried), and why do we organize and store them for posterity?  The easy answer is that we need to find out what they are, to identify them and describe them so we can communicate about them.  We certainly cannot conserve or preserve or even talk about species if we do not know they exist. This is particularly important in the tropics where so many different species have evolved, and especially in areas like Sâo Tomé and Príncipe that have never been fully explored by biologists.  An added note is that for a biologist to know that a species is new and undescribed, he has to know all the related species that it isn’t and then demonstrate it!

It is a fact that a lot of things in the tropics that look alike are not at all related; conversely, some critters that look radically different are, in fact, just variants of the same species.

The botanists of course confront similar questions. Below are two species of the genus Impatiens.

(l) T. Daniel phot – GG IV; (r) M. Nadel phot – GG VI

Both species are high elevation forms described a long time ago: I. manteroana is thought to be endemic to Príncipe, while I. thomensis is known only from Sâo Tomé. But are they really different species? And if so, are they each other’s closest relatives?  We do not yet have material of the former, but this is a question we can answer next year through DNA analysis. The specimen on the right was photographed high on the Príncipe mesa, which is one of the reasons it is a target area for next year.

Below is an island example of two species that look very much alike but are definitely not the same:

D. Lin phots: GG I, GG II]

These are photographs of small leaf-litter skinks of the genus Afroablepharus. The specimen above was collected on Sâo Tomé during GG I and the one below came from Príncipe (GG II).  While they look identical, they are actually two different species as shown by colleagues of ours who were working on the molecular level: extracting DNA from small bits of tissue (probably tail tips) the two species were shown to be genetically quite different.  The one from Príncipe was described over 160 years ago (A. africanus), while the one above, from Sâo Tomé, remains unnamed. This is most frustrating as even though we know they are separate species, we cannot describe the new species yet because the Sâo Tomé animals from which the DNA was analyzed were not collected.  It is a complicated situation that both groups of workers together are trying to resolve at this time.

Another example can be found in the island geckos about which I have written before.

From public presentation by E Miller. CAS Big Kahuna phot (same specimens from above and below).

For over one hundred years, the geckos from both islands that lack thumb nails were considered to be the same species, Hemidactylus greeffi, originally described from Sao Tome.  Our same colleagues noted that the two were genetically different but again failed to take whole samples and so could not describe the Príncipe species as new.  It was not until we closely examined specimens in our Academy collections from both islands that we found many morphological differences between the two, which strongly supported the genetic evidence of our colleagues.  The animal on the right is now  known as Hemidactylus principensis, yet another island endemic. As luck would have it, the paper was published while we were on Principe!

The smaller specimen on the right in both views is also what is known as the holotype; i.e., it is the single animal that is described in minute detail that becomes the “name bearer”.  All geckos collected from the islands and identified as H. principensis will be based on the description of this particular specimen; holotypes are the most important specimens in any collection.

In our collection, which is probably the fifth largest in the world, all holotypes are housed separately and identified by a blue ribbon.

Part of Herpetology collections rooms; holotypes above right, paratypes below right. RCD phots.

Another question often asked of museum scientists is “why do you have to collect so many?”  The answer is that species vary; no two members of the same vertebrate species are identical.  This is why we include additional specimens in a species description.  While the holotype or “name bearer” is usually a single animal in a standard description, other members of the same purported species, hopefully from the same place, are also described in some detail in order to account for individual variation.  These are usually designated as paratypes; in the Academy collections, they are always designated by red ribbons [above] and are the second-most important.

Yet another frequently asked question is, “do you have to kill the specimens?”  The answer lies in the fact that not all characters (similarities and differences) are observable from the outside.  With animal groups like frogs, one has to look deeper, and this is impossible with living specimens. Below is a collage of some of the sorts of characters I had to examine in determining the relationships between members of African tree frogs of the family Hyperoliidae— found in Africa, the Seychelles and Madagascar.

All RCD phots.

Notice that the x-ray in the lower right hand corner revealed to us that the two geckos mentioned above not only lack thumb nails, they lack the entire terminal bone of the thumb! (the new species, Hemidactylus principensis, is on the left). So far as we know, they are the only two members of the genus Hemidactylus, (90+ species) that exhibit this characteristic.  This might suggest they are each other’s closest relatives, but we are in the process of determining that by further DNA analysis that includes other closely related species.

During GG VI we did another kind of collecting:

Rayna Bell, Cornell University. A. Stanbridge phot – GG VI

Notice that in her left hand, Rayna Bell is holding an adult Sao Tome giant treefrog (Hyperolius thomensis), while in her right she has a cotton swab.  She swabbed the skin of each frog she collected a number of times in a number of places in order to detect the presence of chytrid fungus. The swab will also detect the actual infection load if the fungus is present.  This is the first attempt at detecting the fungus on the islands of Sâo Tomé and Príncipe, and we do not yet have results. It is certainly present in other areas of Africa. Batrachochytridium dendrobatidis (Bd for short) is a fungus that has been implicated in the mass die-off of populations of frogs in many parts of the world.  Frog skin is a living membrane through which gasses and water can freely pass; while the mechanism is not well-known, the fungus seems to totally disrupt these functions causing the demise of the infected frog.

 

Cross section of Bd infected frog skin.  (A) are sporangia with zoospores visible. (B) tube through which zoospores are released to the environment. Phot courtesy of A. Pessier, U. Illinois

Another real value to collections is the fact that past history can be discovered through our specimens. It turns out that Bd can also be detected by swabbing alcohol preserved specimens regardless of age, although the resulting data are not quite so informative as samples from living material.  Below is Dr. Dave Blackburn’s “chytrid crew” (mostly undergrad and graduate students) swabbing specimens collected from the Impenetrable Forest of Uganda many years ago.  Dave is our new curator in herpetology and a real expert on Bd.

Dave Blackburn’s “chytrid crew”.  D. Blackburn phot.

Every trip to these small amazing islands yields new discoveries. We are planning our next expedition for 2013 and excited at the prospect of the new stuff we will find.

Here’s the parting shot.

Autonomy Day in Principe, 2012 A. Stanbridge phot, GG VI

PARTNERS

We gratefully acknowledge the support of the G. Lindsay Field Research Fund, Hagey Research Venture Fund of the California Academy of Sciences, (GG I, II), the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging (GG III-V), STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bomfim, and Salvador Sousa Pontes of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to collect and export specimens for study. Special thanks for the generosity of private individuals who made the GG III-V expeditions possible: George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor, Velma and Michael Schnoll, and Sheila Farr Nielsen; GG VI supporters include HBD of Bom Bom and the Omali Lodge for logistics and lodging, The Herbst Foundation, The “Blackhawk Gang,” the Docent Council of the California Academy of Sciences in honor of Kathleen Lilienthal, Bernard S. Schulte, Corinne W. Abell, Prof. & Mrs. Evan C. Evans III, John and Judy Sears, John S. Livermore and Elton Welke.

Our expeditions can be supported by tax-deductable donations to “California Academy of Sciences Gulf of  Guinea Fund”.

 

 

The Race: Our Omali Base, Year’s Odds and Ends

Year’s end and things are busy, even in Academia.   Here at the Academy, we are already in planning mode for GG VI but more on that in coming months.  We are awaiting the publication of more of our discoveries, and I will report them here as they appear.  In the meantime this is a good opportunity to thank all of you who have helped make next year’s expedition a probability: the Herbst Foundation, the “Blackhawk Gang”, and the California Academy of Sciences Docent Council.

As readers know, our mission is not only to discover and scientifically describe what is on these wonderful old islands but to let others know about it, especially the citizens.   But, this also includes the business visitor and tourists primarily interested in fishing or ocean activities.  The neat unique critters we are studying are not just isolated up in the higher reaches of the forest; many can be found right downtown.  You just have to look.

toes by velma

The Omali Pool [photo and toes- V. Schnoll, GG V]

On the beach of Praia Lagarto, between the airport and downtown São Tomé, lies the Omali Lodge.  Originally built by a Mr. Hellinger, I remember it in its original incarnation as the Marlin Beach Hotel, one of the best bars in the islands– a real gathering place.  It is small and quite upscale but it retains its original flavor.  Folks who know the islands or have been well informed stay at the Omali; it attracts rather fascinating people.

The Omali is pretty fancy digs for a bunch of bush biologists like us but luckily, the Omali’s owners have supported our work by allowing us to stay there during our last three expeditions.  As comfortable and friendly as the Omali is, the central thing for our work is a dependable power source (although a post-fieldwork dip in the pool is not too shabby!)

oMALI WECK

The Omali [Weckerphoto, GG III]

So as a new visitor, if you walk through the foyer and bar out to the back to the pool, you will first be struck by the enormous coconut palms.  Ignore them for now; to the left around the back of the kitchen, and behind the rockwork in the pool are several other palm-like trees that aren’t!

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screw pines, Pandanus thomensis. fruit (r), prop roots (l)  [T. Daniel, GG III, IV]

These are the São Tomé screw pines, Pandanus thomensis.  You can tell them from the palms by the fact that the base of each tree is supported by a number of prop roots (see right, above).  Obviously, these are neither pines nor coconuts; the important thing to know is that these trees are found only on São Tomé, nowhere else in the world.

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Trachylepis maculilabris. [D. Lin, GG II]

As you walk along the pool, the first quick movement in the grass is likely to be a speckle-lipped skink, particularly common during the heat of the day.  These lizards are not unique to the islands but they are very good dispersers across oceanic barriers, and they are found on many of the Atlantic and Indian Ocean islands.  Some of our colleagues have looked at the genetics of the São Tomé and Prìncipe skinks and suggest that while they are not endemics, they have been on the islands since long before man arrived.

Lygo thomensis  JU III

Lygodactylus thomensis [J. Uyeda, GG II]

On the walls surrounding the pool and rooms lives the São Tomé day gecko, Lygodactylus thomensis, which shuttles in and out of the shade in search of insects.  Most geckos are nocturnal creatures, but this group is secondarily diurnal.  L. thomensis is a true endemic whose ancestors probably reached São Tomé millions of years ago; the same is true of its closest relatives, the Prìncipe day gecko, L. delicatus, and the Annobon day gecko, L. wermuthi.

Scutellaridae true bug weck

Homopteran true bug [Weckerphoto, GG III]

Most of the Omali plants are ornamentals from other parts of the world of course, but this does not mean they do not harbor fascinating species.  Our photographer on GG III, Wes Eckerman took the photograph above of a homopteran bug on a bush near the Omali pool.   Our entomologists have not been able to identify it beyond the Family Scutellaridae! It is highly likely that an enormous number of the islands’ insects remain to be discovered and described scientifically.

waxbill

Common waxbill,  Estrilda astrild [Weckerphoto, GG III]

cordon bleu

Blue-cheeked cordon-bleu, Uraeginthus cyanocephala [Weckerphoto GG III]

Bird life around the pool is plentiful and entertaining. The most commonly seen birds in the Omali bushes are various finches and waxbills that are of African origin and possibly brought over from the mainland as pets by the Portuguese colonials (above).  But the real specialty is the São Tomé Prinia.  Prinias are Old World insectivorous warblers; there are about 30 species divided between Africa and Asia.  Prinia molleri is the only member of this group in the islands and it is found only on São Tomé, from downtown all the way to the top of Pico at 2,000 meters. As common and seemingly fearless as this endemic little bird is, it is extremely difficult to photograph. It just won’t hold still.

pRINIA

Prinia molleri on Omali window sill [Weckerphoto, GG III]

pRINIA2

Prinia molleri [Weckerphoto, GG III]

Finally, lying around the Omali pool it is impossible not to notice the noisy action up at the top of the palm trees.  Part of the year the palm fronds seem to be inhabited mostly by vitelline masked weavers. Even when they are not around their distinctive nests from the year before are obvious. Males display noisely to attract females to the new nests, which are made annually.

Weaver_Vitelline_Masked_Soitorgoss_Daudi_2007_03_19_2b

Vitelline masked weaver,  Ploceus velatus [Globaltwitchers phot]

These weavers are native but not unique to the islands although some ornithologists recognize them as a distinct race (or subspecies, Ploceus velatus peixotoi) indicating that they may have been isolated from the mainland long enough to be recognizably different from the mainland species.  These weavers are not found on Prìncipe.  All who know them would agree that weavers are a noisy group in general.

When we are working on the islands, usually March-May, the weavers are rather scarce and instead, their place in the palm trees seems to be taken up with the large island fruit bat, Eidolon helvum. These large bats are common on the African mainland where they are migratory; the São Tomé populations are thought to be the same species but do not migrate.  They are eaten by many local people.

Bat Eidolon helvum

Eidolon helvum at the Omali [RCD, GG V]

An hour or so at the Omali pool at the right time of year is enough to learn that Eidolon is a very noisy animal as well.  They seem to argue and fuss all day when they should be sleeping; the sight of the entire group flying off to feed at dusk is unforgettable.

velma

Fruit bats leaving the Omali at dusk [V. Schnoll phot. GG V]

Bats are a group much in need of genetic study.  There are a number of endemic species recognized by anatomical characters, but in most cases their true species status has not been tested molecularly as we have done with the Sao Tome shrew (see earlier blogs).  The expert on the bats of these islands is my colleague Dr. Javier Juste of the Doñana Institute in Seville, Spain.  In an earlier blog I reported that Dr. Juste was involved in the description of a new pipistrelle bat from Prìncipe – this is not yet published and is based in part on genetics. During the past few weeks, I have sent Javier some images of bats we have taken during past expeditions, and he has kindly tried to identify them for us.

bats Nova Cuba

Hipposideros bats at Nova Cuba, Principe [Weckerphoto, GG III]

This is a group of bats we found at the old plantation of Nova Cuba, on Prìncipe. Currently recognized as Hipposideros ruber guineensis, they are thought to be a race of the red bat common on São Tomé but it would not surprise me if further analysis might prove them to be a distinct species.

Hipposideros ruber guineaeensis

Nova Cuba. Hipposideros ruber guineensis [Weckerphoto, GG III]

The photo below was taken by Wes during the day, on the ridge above Lagoa Amelia at about 1400 meters on São Tomé. Javier thinks it might be the endemic Hipposideros thomensis.

H. thomensis Lagoa Amelia

Hipposideros thomensis above Lagoa Amelia. [Weckerphoto, GG III]

A final note on spiders; two previous blogs this year have dealt with spiders we have found in gardens, one of which turned out to be an endemic species.  A few days ago, my colleague Angus Gascoigne of the Instituto Superior Politecnico sent me several photos of the spider below:

argiope1

Argiope orb weaver [Manuel Morais phot. 12/2011]

I took the photos in to our spider experts and they got quite excited.  It is an orb weaver of a widespread genus but “this one is really different!”  I suppose I should not be surprised, and Angus is collecting more as I write.

For all of you who observe them, Happy Holidays!

Here’s the Parting Shot:

parting

The Raison d’Etre!

PARTNERS

We gratefully acknowledge the support of the G. Lindsay Field Research Fund Hagey Research Venture Fund of the California Academy of Sciences, (GG I, II), the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging (GG III-V), STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bonfim, and Salvador Sousa Pontes of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to export specimens for study, the support of Bastien Loloum of Zuntabawe  and Faustino Oliviera, Curator of the Herbarium at Bom Sucesso. Special thanks for the generosity of private individuals who have made the last three expeditions possible: George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor, Velma and Michael Schnoll, Sheila Farr Nielsen, Corinne W. Abel and Mr. and Mrs. John Sears.   Our expeditions can be supported by tax-free donations to “California Academy of Sciences Gulf of Guinea Fund”.

The Race: New Species, New People and Intriguing Biogeography

Lots of news this time. First, graduate students of the University of California, Santa Cruz and California State University, Monterey Bay teamed up to do a most excellent on-line presentation of our work in the Gulf of Guinea Islands, called Documenting Eden; it includes a slide show and can be found here: http://sciencenotes.ucsc.edu/2011/pages/eden/eden.html
On the biodiversity education front led by Velma Schnoll, we are working on several projects including a coloring book of endemic species, a lesson plan to support our poster project of GG V and possibly an animated cartoon featuring the fabulous yellow caecilian, cobra bobo, as “spokescreature” for the unique species on the  islands.
Some great news is that the Academy has hired three new Curators in Microbiology, Herpetology and Ichthyology.

rocha

Dr. Luiz Rocha, CAS Ichthyology Section.  RCD phot.

Dr. Rocha (above) is a marine ichthyologist and brilliant underwater photographer who has already worked in São Tomé and Príncipe. He was a member of a National Geographic-sponsored marine expedition in 2006 which occurred shortly after our CAS GG II expedition concluded.  The results were published in the journal Zootaxa a year later and included many of the fishes already collected on our first two expeditions by Dr. Tomio Iwamoto and others of us.

I walked into Luiz’ lab a couple of weeks ago just to talk, and found he was just finishing up the description of a new species of parrotfish from Säo Tomé, based on three specimens we collected  on earlier CAS expeditions!

sparisoma1

Sparisoma sp. nov., new São Tomé parrotfish. L. Rocha phot

The holotype specimen (the single “name bearer”) was collected by Dr. Tomio Iwamoto in 2006 (GG II) by hook and line from Ned Seligman’s pier on Praia Francesa.   Readers of this blog will remember that Ned is the head of an island NGO called STeP UP through which we have worked since the beginning in 2000; he is also a life-long friend of mine.

praia-francesa

Chez Ned (l) and the author (r),  Praia Francesa  T. Daniel phot. GG IV

The additional specimens (paratypes) include another collected directly from a beach seine by Tomio and I in 2001(GG I), and one purchased from the town fish market by Dr. John McCosker and David Catania in 2009 (GG IIIB).   It is very exciting to have a bright new colleague here at the Academy who is interested in the Gulf of Guinea; the manuscript is in review and as always, we will send the published article to the islands.

js-rcd-iv1

Jim Shevock, Laguna Azul.  RCD phot GG IV

Meanwhile, our tireless moss guru, Jim Shevock, and colleagues from Dresden and Hungary have published another paper on the GG IV bryophyte collections; we have already sent the paper to the islands.  As a result of Jim’s GG IV work, the authors report 18 species of liverworts and hornworts  (moss relatives) as new for the Republic of São Tomé and Príncipe overall.  With respect to the two islands, 13 new species records have been found new to Príncipe and 16 new for São Tomé.  None of these species is new to science, but the country list for liverworts and hornworts is now 147 species, a much greater diversity than was known.

My lab has been quite active all summer.  Eden Maloney returned from UCLA to further refine the genetic component of her work on the endemic São Tomé shrew, Crocidura thomensis; this research includes the ecological work by our colleague Ricardo Lima, a doctoral student at  Lancaster University and genetic work by Dr. Brian Simison, Director of our Center for Comparative Genomics.

Much of our recent focus in the lab has been on the endemic, Greeff’s  giant gecko, Hemidactylus greeffi,  described from São Tomé by the Portuguese biologist Bocage in 1886.

greeffi-culvert

Greeff’s giant gecko (Hemidactylus greeffi), road culvert, Praia Mutamba. D. Lin phot. GG I

This species is unique among the 90+ members of the genus Hemidactylus,  in that it lacks the claw and the actual terminal bone (phalanx) of the thumb.

foot

Bom Bom, Principe Weckerphoto –  GG IV

Evolutionary loss of the first claw is known from a species in Brazil, H. brasileanus but until now, absence of the underlying terminal phalanx has been thought to be unique to Greeff’s giant gecko.

animaldiversityummzumichedu

Hemidactylus brasileanus phot: animaldiversity, U. Michigan

H. greeffi was thought to inhabit both São Tomé and Príncipe islands but in 2005, our colleague, José Jesus of the University of Madeira and his co-workers compared the genetics of samples from both islands and found significant differences in mitochondrial DNA sequence between them.  However, they did not find any differences in the nuclear genes they examined and thus deferred describing the Príncipe individuals as new.

In June, I tasked my Summer Systematics Intern, Elizabeth Miller of UC San Diego, with doing a detailed anatomical examination of our collections of the geckos from both islands, along with a molecular study of the two populations using the data kindly sent to us from Dr. Jesus but also employing new, faster-evolving nuclear genes.

Long before the genetic analysis was completed, Elizabeth found obvious and consistent morphological differences between the two populations.   In fact, these differences are so striking that I think if anyone had ever done careful comparison of the bodies of the two sets of geckos, the Príncipe population would have been described as a separate species long ago, DNA evidence notwithstanding.

gecko-comparison

left, Sao Tome, D. Lin phot- GGI;  right, Principe, Weckerphoto GG III

Among the many character differences she found was in iris color!  H. greeffi of São Tomé has beautiful light, moss-green eyes, while in the Príncipe population, the eyes range from gold to light copper.  This would seem to be an obvious, readily recognizable difference, but it must be remembered that except for Dr. Jesus and his colleagues, all previous scientists who have studied these geckos have been dealing with preserved specimens, in which eye color is invariably lost—in fact much body pigmentation is lost in museum preservatives .

Subsequent DNA sequence data generated by Elizabeth in our Center for Comparative Genomics confirmed that José Jesus and his colleagues were correct; the Príncipe populations do indeed represent a separate, undescribed species.  At the same time, however, they share with H. greeffi of São Tomé the absence of the terminal phalanx of the thumb; this strongly suggests that H. greeffi and H. sp. nov. are each other’s closest relatives (but more on this below).

lizzie

Miller (back left) presenting our results to the Summer Systematics Institute, August 2011 RCD phot

Currently Elizabeth and I, along with Anna Sellas of our CCG molecular lab are completing a formal description of the new gecko from Príncipe.  The two gecko species, along with their purported nearest relatives present quite an interesting biogeographical question, now being addressed by my graduate student, Dashiell Harwood.  At first glance, our molecular results suggest that the ancestor of both H. greeffi and the new Príncipe species colonized São Tomé first, then later made it across to Príncipe but we have a number of reasons for doubting this scenario.   Part of Harwood’s project will be to employ Elizabeth’s data plus additional genes and deeper analysis in order to answer this initial question.  But if we can obtain appropriate samples, there is a much broader gecko issue we can study.

aa-clade

cladogram from Bauer et al. (2010) Mol. Phylo. Ev. 57

Above is a small subset of a much larger cladogram of Hemidactylus species done by our colleague Dr. Aaron Bauer of Villanova University and his co-workers.  The highlighted box indicates H. greeffi and its closest known relatives, H. longicephalus of the African mainland (also São Tomé) and H. brasileanus of South America.  The species examined in Bauer’s study did not include samples of our new gecko from Príncipe Island.

atl-disprs

African-Atlantic partial distribution.

The image above is a visual perspective of the rough distributions of four species of Hemidactylus, including Príncipe.  If the cladogram is a true reflection of the relationships of three of the four species here, and if the Príncipe gecko is indeed, H. greeffi’s closest relative and fits in as we surmise, then the common ancestor of all four species must have crossed the Atlantic, from the African continent to northern South America.   This is not a new idea and was proposed by Carranza and Arnold in 2006, who stated that during the last 15 million years, African lineages have crossed the Atlantic by random (natural) dispersal at least twice.  The likelihood of this long-range dispersal is strengthened by a look at the dominant Atlantic currents.  Readers of the blog will recognize the South Equatorial Current as the same one we invoke as providing a “freshwater pathway” for rafting from the Congo and Niger Rivers on the mainland, straight through the Gulf of Guinea archipelago (see Oct and Nov, 2008 blogs and Measey, et. al (2007) Journal of Biogeography 34.)

atlantic_ocean_currents

Major Atlantic Ocean Currents

In the Carranza and Arnold paper, H. longicephalus and three additional Brazilian species were employed, as was “H. greeffi”; however, the tissues we sent the authors were from Príncipe, before we knew the two island populations were distinct.  So Harwood’s graduate work should shed some light not only on the relationships between these geckos, but their geographic origins and history.

Here’s the Parting shot:

sunset-rwSunset on Bom Bom Island, R. Wenk phot.  GG IV

PARTNERS

We gratefully acknowledge the support of the G. Lindsay Field Research Fund Hagey Research Venture Fund of the California Academy of Sciences, (GG I, II), the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging (GG III-V), STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bomfim, Salvador Sousa Pontes and Danilo Barbero of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to export specimens for study, the support of Bastien Loloum of Zuntabawe  and Faustino Oliviera, Curator of the Herbarium at Bom Sucesso. Special thanks for the generosity of private individuals who have made the last three expeditions possible: George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor, Velma and Michael Schnoll and Sheila Farr Nielsen. Our expeditions can be supported by tax-free donations to “California Academy of Sciences Gulf of Guinea Fund”.

The Race: Really Weird Island Snakes

A wormsnake from Kenya (Leptotyphlops drewesi).   Phot. D. Lin, CAS

In these accounts, I have written a fair amount about the two species of island house snakes (Lamprophis-cobra jita) that Lisette is still analyzing and a bit on the supposedly introduced cobra on São Tomé (Naja melanoleuca – “cobra preta”);  I have also mentioned the fact that each island also has a diurnal green snake, endemic  but unrelated to each other (Hapsidophrys principis, Philothamnus thomensis –“cobra sua sua”.   However, there are three additional snakes that I have not mentioned much: these are the so-called blind- or worm snakes.  Collectively, their technical name is the Scolecophidia, and the group is considered primitive relative to other snakes.  As their common names imply, all have reduced or no vision, virtually all of them are burrowers; they are small as snakes go and blunt at both ends, and there are about 300 species in three families found world-wide in tropical and many subtropical regions.

The fact that they are burrowers (fossorial), like the endemic São Tomé caecilian, Schistometopum thomense –“ cobra bobo”, lends credence to our 2007 hypothesis that some of the Gulf of Guinea endemics were carried to the islands from mainland Africa on very large floating chunks of riverbank from either the Niger or the Congo.  Burrowing legless vertebrates are unlikely to be found floating on logs or being carried by high winds!

Proposed riverbank raft (Measey, et al., 2007). Illustration: Richard E. Cook

There are three endemic blindsnakes on the oceanic Gulf of Guinea Islands: The beatiful golden blindsnake, Typhlops elegans is endemic to Príncipe island.  It is often confused by locals with the São Tomé burrowing caecilian, as its Kreo name implies: “cobra bobo do Príncipe.

Typlops elegans, the “cobra bobo do Principe.”  Weckerphoto GG III

Typlops elegans. D. Lin phot. GG II

Two endemic blindsnakes inhabit São Tomé exclusively, and as you can see they are extremely similar in appearance.

Fea’s wormsnake, Rhinotyphlops feae. D. Lin phot. GG II

Newton’s wormsnake, Rhinotyphlops newtoni. RCD phot. GG I

The reason I have not written much about them is that they are rather poorly known. Most species are small and difficult to work with, in that the characteristics that might serve to distinguish them are also very small and nearly impossible to discern without magnification.  My colleague, Dr. Van Wallach, of Harvard University is probably the current world authority on these wormlike snakes, and it has taken much of his career to understand them; many of the characteristics he has studied are internal.

Colleagues of mine have just published a major work on one of the families, the Typhlopidae,  in Biology Letters, a distinguished international journal.  Prof. Blair Hedges kindly gave me permission to reproduce the figure below, and I am discussing it here relative to our island work in order to show how the work of others can add to, support or even falsify one’s own– it is how science proceeds.from Vidal, Marin, Morini, Donnellan, Branch, Thomas, Vences, Wynn, Cruaud & Hedges. 2010 Biology Letters 6:558-561

This is not as complicated as it may seem although it will be difficult to read at low resolution.  As with other cladograms, each of the names on the far right column  represents a single species clustered with its nearest relative(s); thus it is a “picture” of proposed evolutionary relationships.  This figure also contains estimates of when each lineage and its nearest relative split from their common ancestor (time divergence)—the common ancestor is indicated by a black dot (node) and the length of each branch linking two species is an indication of time.  Actual time in millions of years is given on the very bottom, along with the names of the geologic periods in vertical colored bars (blue= Jurassic; light green = early and late Cretaceous (K); orange  = Paleogene, and yellow, the most recent =  Neogene).  The authors have also provided diagrams (upper left) of the relative positions of the continents during the breakup of Gondwanaland.  The major points of this study are (1) that the common ancestor of all scolecophidians dates back 150 million years to the Jurassic Period (before the breakup of Gondwanaland), (2) that the ancestor of the modern Typhlopidae originally existed on an early landmass the authors call Indigascar (Madagacar + India) back in the Late Cretaceous, and (3) that the presence of their modern relatives in South America, Australia and the West Indies is most likely the result of a number of overwater dispersal events (like rafting), including a major western transatlantic one.

Vidal and the other authors included samples of the Gulf of Guinea Islands endemics which we collected during GG I and GG II, and their results are of great interest to us as we try to understand the origins of the Gulf of Guinea Islands biodiversity.

Expanded view of African clade from Vidal et al. Principe species in blue; Sao Tome species in red.

Distribution of the two Sao Tome wormsnakes and nearest relatives.

Here is the disjunct pattern that has frequently appeared when we look at the evolutionary relationships between Gulf of Guinea island endemics and their African mainland relatives; first, note that Rhinotyphlops newtoni and R. feae appear to have diverged from their common ancestor only a few million years ago.  Since, the minimum age of São Tomé is regarded as about 13 million years, it seems likely that this split occurred on the island, possibly as a result of volcanic events which isolated two populations of the ancestor from each other.  This is a more likely scenario than separate colonization events from the mainland.  However, the nearest relatives of the island species are a clade (sister-group) comprising R. unitaeniatus of East Africa and R. lalandei of southern Africa, and a look at the branch lengths of this sister-relationship suggests that, if the time divergence estimates  in this publication are correct, the common ancestor of both groups existed on the mainland over 50 million years ago.

Distribution of Principe wormsnake and its nearest relatives.

The situation with the beautiful Príncipe endemic, Typlops elegans is somewhat unclear, since the true distribution of its nearest relative, T. angolensis, is not known with certainty; the latter is said to occur from coastal Cameroon, south to Gabon and Angola and west to western Kenya, but these specimens have never been systematically examined.  Moreover, African distributions as broad as this one frequently turn out to be made up of the distributions a number of similar “cryptic” species.  But assuming that T. angolensis does have this distribution, that the tree is accurate, and the time divergences therein are reasonable estimates, one would naturally conclude that the ancestor of “cobra bobo do Príncipe“ reached that island and diverged from mainland T. angolensis during the past few million years.  If branch lengths are accurate it would appear this happened at roughly the same time as the two São Tomé endemics were diverging from their common ancestor.  Even though Príncipe, at 31 million years, is more than twice as old as São Tomé is geologically, this is not an unreasonable hypothesis.

This cladogram also suggests that these two blindsnakes share common ancestry with an unidentified species (specimen) collected at Lwiro, Democratic Republic of the Congo.  This interests us because this locality is close to the Itombwe Highlands, which are, geologically, very, very old, dating back to the Mesozoic.

On a different tangent, our island biodiversity posters are nearing completion, and that will be my next topic.

The parting shot:

Our work in Paradise.  Sao Tome, Weckerphoto – GG III

PARTNERS

We gratefully acknowledge the support of the G. Lindsay Field Research Fund, Hagey Research Venture Fund of the California Academy of Sciences, the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging, STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bomfim, Salvador Sousa Pontes and Danilo Barbero of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to export specimens for study, the continued support of Bastien Loloum of Zuntabawe  and Faustino Oliviera, Curator of the Herbarium at Bom Sucesso. Special thanks for the generosity of private individuals, George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor and Velma and Michael Schnoll for helping make these expeditions possible.  Our expeditions can be supported by donations to “California Academy of Sciences Gulf of Guinea Fund”.

The Race: Unique Shrew Confirmed: The Magic of Molecules

The summer is almost over, and we have made some wonderful progress in our race to discover more island uniqueness before development changes everything.  When I say “we”, I mean all the dedicated scientists, students and educators involved in our island biodiversity race for the past ten years. However, at the moment the laurels rest squarely on the head of Eden Maloney from the University of California at Los Angeles. Eden has been my intern at the California Academy of Sciences this summer, where she is known as “The Shrewster.”

Crocidura thomensis (l); Eden Maloney, UCLA

One of our most intriguing questions has been whether the supposed endemic São Tomé shrew, Crocidura thomensis, is really endemic, found nowhere else in the world. This would suggest that its ancestor arrived on the island by natural means (rafting?) a long, long time ago.  The alternative (and more likely) hypothesis is that it was brought to the islands, perhaps inadvertently, by the Portuguese during their 500 years of intense commerce on the islands, and the scientist who described it as unique was in error.

This is an important issue, because mammals, with the exception of some bats, are notoriously poor over-ocean dispersers because they are endotherms, needing to maintain a constant body temperature. Moreover, among mammals, the very worst candidates as island colonizers are shrews.  A shrew’s metabolic rate is so high that it must eat every four hours or die from heat loss; thus no competent biologist would predict the presence of such a creature surviving an extended crossing to colonize an oceanic island.

José Vicente Barbosa du Bocage (1823 – 1907); Wikipedia image

Crocidura thomensis was originally described in 1887 by J. V. Barbosa du Bocage, the curator of Zoology at the Museum of Natural History in Lisbon. He based his description on anatomical features such as the large size of the shrew’s feet and ears as well as the particularly long snout. We decided to do a molecular (genetic) test of Bocage’s hypothesis that C. thomensis is found only on Sao Tome and nowhere else in the world. Thanks to the kindness of our friends from the Ministry of the Environment, Arlindo Carvalho, Vitor Bomfin and Salvador Pontes, we were granted permission to receive some shrew specimens collected by our colleague, Ricardo Lima of Nova Moca and to export them to the Academy where Eden did DNA analysis of them. She also included two shrews we collected on Príncipe during GG II (2006). These have long been thought to be an introduced mainland species.

Eden was able to take advantage of a massive molecular study published three years ago by Dr. Sylvain Dubey of the University of Lausanne and his colleagues.  Dubey’s study included 139 members of the shrew Family Soricidae from all over the world, but of course he lacked examples of our island shrews. Eden contacted Dr. Dubey, who was most helpful, and she was able to use the same four genes in her analysis that Dubey used in his larger study. Below is an image of the alignment of the DNA sequences of Dubey’s samples together with our island samples.

Shrew DNA sequence alignment. E. Maloney construct.

Maximum Likelihood Tree; E. Maloney Construct

Above is a cladogram, basically a picture of relationships- it includes the majorityof Afrotropical species and most Asian species that Dubey sampled, plus our island critters. Each line represents a species (or sample), and the lines that are joined together at the base (node) represent species (samples) that are each other’s closest relatives. The blue arrow is C. thomensis, our São Tomé shrew, the red is our Príncipe samples.  While both are members of the same subset of the Afrotropical clade (related groups of lines), note that they are only distantly related to each other. There a number of lines (species) between them, and there are a number of distinct lineages (clades) within the Afrotropical group.

Afrotropical clade III; Eden Maloney construct

Above is a representation of Eden’s Afrotropical Clade III, therelated group within the broad African species clade that includes both our island samples.  Our São Tomé species samples are in the red box, and notice that their nearest relative is a mainland species called Crocidura cyanea, a shrew that ranges from Angola, Botswana and Mozambique south into South Africa.  C. thomensis is genetically distinct enough from this (it’s nearest relative) and all other species in the tree for us to say with confidence that it is a true endemic.  From this we infer that the common ancestor of C. thomensis and C. cyanea somehow reached the island a long, long time ago, long enough for it to have been isolated from the mainland for a great enough period of time to have accumulated enough genetic change so that it is now recognizable as a distinct species. Assuming that our study is accurate and our analysis is correct, Crocidura thomensis is the Gulf of Guinea oceanic islands’ only endemic terrestrial mammal.

Sao Tome’s only endemic terrestrial mammal, Crocidura thomensis; R. Lima phot. 2009

We are not quite ready to publish these results though.  There is still the problem of the two Príncipe samples, called C. poensis (blue box in the Afrotropical cladogram). The shrews on this island have long been thought to be this particular mainland species but the name is an assumption on our part; there are some missing sequences of C. poensis in Dubey’s study, and until we can clarify the situation, we do not know the correct name for the Príncipe shrew; it is probably either C. poensis or C. batesi, both mainland forms.  However, the genetic differences between our Príncipe samples and the other species in Afrotropical Clade III are so small as to strongly suggest that the species is not endemic but rather a recent arrival.

Ricardo Lima in Europe; unknown phot.

Our colleague in this study is Ricardo Lima, who has appeared in this blog a number of times.  Ricardo is a doctoral candidate at the University of Lancaster, has been doing his fieldwork on Sao Tome for several years and is an excellent biologist who is deeply concerned with the unique biodiversity of the islands.  He has an excellent blog: http://riscas83.blogspot.com/

Ricardo Lima on Sao Tome;  phot. R. Rocha

Ricardo not only re-discovered the São Tomé shrew (incorrectly thought to be rare), he has also learned more about this species that has ever been known before.  He has made and plotted numerous sightings of the species during his fieldwork and has been able to learn a great deal about its abundance and natural history.  So, Eden, Ricardo and I will collate his ecological data with our genetic data and publish our results when the remaining issues are all resolved.  One other item: I have suggested, perhaps rashly, that Crocidura thomensis may be the only endemic oceanic island shrew in the world; further investigation is needed.

Anna Sellas, Lab Manager, Center for Comparative Genomics; RCD phot.

We are able to ask and answer such finely-tuned, detailed questions of genetic distance about the unique biota of São Tomé and Príncipe because we have the appropriate tools and wonderful people in our lab. The Center for Comparative Genomics is an integral department of the California Academy of Sciences.  Headed by Dr. Brian Simison, the lab is managed and run by Anna Sellas, a fine biologist and most able teacher of molecular techniques. Dana Carrison, a member of GG III who did her MSc on island barnacles also works in the lab and greatly assisted Eden.

Grad Student Scientists with Gulf of Guinea Projects.  RCD construct

A number of our interns and grad students who have worked in the field with us have done their analyses of São Tomé and Príncipe projects in the CCG. Four of mine, I am enormously proud to say, have entered or completed doctoral programs– they appear above. Some of their projects have been published, the rest are still in preparation.

The parting shot:

Haul-out,  south of Neves.. R. Wenk Phot –  GG III

PARTNERS

We gratefully acknowledge the support of the G. Lindsay Field Research Fund, Hagey Research Venture Fund of the California Academy of Sciences, the Société de Conservation et Développement (SCD) and Africa’s Eden for logistics, ground transportation and lodging, STePUP of Sao Tome http://www.stepup.st/, Arlindo de Ceita Carvalho, Director General, and Victor Bomfim, Salvador Sousa Pontes and Danilo Barbero of the Ministry of Environment, Republic of São Tomé and Príncipe for permission to export specimens for study, the continued support of Bastien Loloum of Zuntabawe  and Faustino Oliviera, Curator of the Herbarium at Bom Sucesso. Special thanks for the generosity of private individuals, George G. Breed, Gerry F. Ohrstrom, Timothy M. Muller, Mrs. W. H. V. Brooke, Mr. and Mrs. Michael Murakami, Hon. Richard C. Livermore, Prof. & Mrs. Evan C. Evans III, Mr. and Mrs. Robert M. Taylor and Velma and Michael Schnoll for helping make these expeditions possible.  Our expeditions can be supported by donations to “California Academy of Sciences Gulf of Guinea Fund”.