The day Hurricane Isaac rolled through Baton Rouge (Aug 28th)
saw the publication of what I consider the best project that I’ve ever been a
part of: a paper showing the sister relationship between Milyeringa, a genus of cavefishes from Australia and Typhleotris, a genus of cavefishes from
Madagascar. [Get the original open access paper by clicking here: Chakrabarty et al. 2012] I’d like to tell the tale of the Malagasy trip that was the
inception of the project and to tell a bit about the story behind the paper
before diving into the science.
When I was a young boy dreaming of being a zoologist, I
dreamt of going to far off countries and discovering wildly amazing new
creatures in places no one has ever been. In my childhood nightmares I feared
the dark and being trapped in small spaces. My trips to Madagascar and
Australia fulfilled both the dreams and nightmares of my youth.
Sinkhole fever and
the Death Goby.
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| Fig1. The dreaded sinkhole. |
I went to Madagascar shortly before my postdoc ended at the
AMNH (American Museum of Natural History) and after I had been hired at LSU (Louisiana
State University) in the summer of 2008. It was a weird period in my career
when I was probably focusing more on the future than the present. My wife and I
were in the process of buying our first house; in fact I was signing documents (including
my LSU contract) up to the moment I was getting into the cab headed to the
airport. The trip to Madagascar came at the perfect time for me; I was done
with the stresses of having to find a job, and was ready for something to highlight
the end of my old position. As luck would have it the Constantine S.
Niarchos Expedition Fund provided my postdoctoral mentor, John Sparks
(Curator, AMNH), with a grant to travel to Madagascar and collect blind gobies.
I actually didn’t pay much attention to why we were going to Madagascar, I just
knew I wanted to go: I’ve always wanted to go. My first work in science, as an
undergrad with Melanie Stiassny, was on Malagasy cichlids (Stiassny et al.
2001) and I always saw Madagascar as one of the last remaining wild places on
Earth. I was so busy buying a house in Baton Rouge, negotiating my start-up, and
packing for the trip that I really didn’t know much about the actual taxa we
were after in Madagascar. I had been working on bioluminescent fishes my entire
postdoc and never worked with gobies or caves before. I figured I would
catch-up on these subjects during the plane ride over to Antananarivo
(Tana). As it happened I did more catching up with Scott “Scuppy” Holtz
(now a grad student at Cal State Fullerton)
and Phil Willink (then at the Field Museum) who were joining John and I in the
field. By the time we got around to our first field site (after much stamping
of documents, preparation of materials, shaking of hands, and days of impossibly
slow and shaky driving across terrible Malagasy “roads”) I sort of had an idea
that we would be collecting some rarely seen and poorly understood freshwater
cavefishes, namely two species of Typhleotris.
Most of what we knew about these species was from their original descriptions
(in the 1930s and 50s) and that others had noted that they share a striking
resemblance to the cavefishes of Western Australia. John had done a ton of
research on the caves of the region, and with the help of the wonderful Steve
Goodman, discovered a large sinkhole that was mentioned in a French geologist’s
dissertation that possibly contained blind cavefishes. Sinkholes are not caves,
they are exposed to the open air and sunlight; what is visable is just part of
a larger subterranean habitat (i.e., a karst window). I was horrified and
impressed when I was first confronted by this football-field sized sunken lake
(Fig 1). The vintany, as the locals called it, made my heart sink into my
stomach. ‘What could possibly live down there?,’ I thought to myself. I was
trying not to let my nervousness show when Scuppy secured a flimsy chain ladder
to a dangling tree at the edge of the sinkhole. As luck would have it I went
into the water first while the others secured more equipment. The first part of
the climb down over the lip of the sinkhole was particularly nerve-racking
because you couldn’t see over the edge to your next foothold. The local guides
sat a safe distance away with no interest in getting closer to the insides of
this strange pit.
As I snorkeled I started thinking
of what I would do if I encountered one of the huge Nile crocodiles this region
is famous for. I felt a bit like a miner’s canary, but I didn’t see anything:
no fish, no crocs, no beluga whales. All I encountered were some spiders and
insects and a beautiful view of the deep dark waters below. As I climbed back
up the ladder I saw John and Phil were getting ready to head down. They swam
for a long while and after some 25 minutes John yelled out, “I got one.”
‘Got one, what?’ I thought.
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| Fig 2. A new species of Typhleotris. |
He passed the specimen to Scup who
climbed up the chain ladder with an ease I wish I possessed. I looked at this
little beast, no longer than my pinky, and as dark as a Hershey’s chocolate.
How strange this creature was: it lacked eyes and had a smooth bony head (Fig
2). Why would there be an eyeless fish here? Why is it so darkly colored? The water is clear and sunlight penetrates as
far as you can see; the sinkhole appeared more than 50 meters deep, perhaps
more. What lies beneath, the French geologist’s dissertation told us, was a subterranean
groundwater connection to caves several kilometers away. After some time John
yelled out again: he had gotten another one. Around this time I started to get
nauseous, I had ingested some of the water while snorkeling and it wasn’t
sitting well. I tried not to think about it while I dutifully took photos, GPS
coordinates, and tissue samples. The locals had warned me that this was a
revered site and that I should not urinate near the mouth of the sinkhole. I
didn’t need to pee but I did need to vomit, although the water was clear it was
full of loose vegetation and was effectively a pit trap for anything unlucky
enough to fall in.
I walked out of sight of everyone
and vomited the sinkhole water I had accidentally ingested. I came back to my
notebook, camera and specimen just in time for the second specimen to be
brought up to me. John and Phil who had been swimming for more than an hour
finally came up. This second specimen was dark and eyeless like the first one, and
a similar size. John and Phil told me they had seen others but those
individuals slowly sank away into the deep just out of reach. The dark
coloration is a great camouflage and the fish are certainly aware of their
surroundings, enough so to move away from larger moving objects splashing
around. Were this species white, as most subterranean species are, it would
have been easy pickings for birds that could strike from above and perhaps even
to swimming snakes or other creatures that could handle the initial 30ft
descent.
We were feeling pretty good about
ourselves having collected something amazing from the very first site. We were
in good spirits when we retreated back to our camp. A couple days later when we
started collecting at a new location a little further north it became clear
that all was not well. In deference to my colleagues I won’t replay how sick
the team got, but it was pretty scary stuff - especially given how far we were
from civilization. I think I was spared major illness because I expelled most
of the water I had ingested while snorkeling. We jokingly named the mysterious
illness “sinkhole fever,” but seeing your mentor and friend so ill that you
consider using the satellite phone to call in a helicopter is no joke. The next
day we sent Scuppy and John back to Tana. Scuppy went to a hotel to rest up while
John flew back to New York.
We did
quite a bit more collection after that. Phil and I went to a dozen or so more caves
over the next week and had quite the amazing experience in the southeastern
part of Madagascar. Scuppy, who had recovered well in Tana, was well enough to
join me for a trip to the northern tip of Madagascar (Ankarana) after Phil
departed. In the north, Scuppy and I collected both blind and sighted members
of Glossogobius, sometimes right next
to each other. Those caves in the north
remain the most spectacular places I’ve ever been, but it will always be the vintany,
home of the darkly pigmented “Death Goby,” that will be the defining site of
the trip. [The description of this darkly pigmented form is in press and should
come out later this year.]
Back Home.
On
returning from Madagascar I effectively was done at AMNH and was now a new
faculty member at LSU. All the sequencing and analysis was done at LSU for the
project that would eventually become our PLoS paper. The addition of Matt Davis
as my postdoc, the first person to join my lab in 2010, really transformed how
we viewed our data. I am not a goby biologist, and although we had some gobies
collected we didn’t have enough for a wide-scale global phylogeny. Luckily
there was already a well-sampled phylogeny completed using mitochondrial genes
(Thacker 2009). It was our intention from the start to stick our newly
collected samples in with the previous data available on GenBank. The other
piece of the puzzle was the Milyeringa
from Australia. Several of the genes for this species had been sampled already
for a few specimens loaned to Chris Thacker, but not a large sampling. In my
2009 trip to Australia I collected some additional specimens, including what
turned out to be a new species of Milyeringa
(described in Chakrabarty, 2010). With both pieces of the puzzle sequenced we
discovered what we and others had suspected, these two cave lineages, now separated
by more than 6,000km of Indian Ocean, are sister taxa.
The Paper.
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| Fig 3: Summary of the relationships of Gobiiformes. See original PLoS paper for details. |
The
cavefish paper describing the relationship between Milyeringa and Typhleotris
published in PLoS One includes John
Sparks and Matt Davis (now at the Field Museum in Chicago) as co-authors (Chakrabarty
et al. 2012); everyone contributed equally. The dated phylogeny we present for
Gobiiformes is the only time-calibrated phylogeny of this extremely diverse group
and uses mostly taxa that had been sampled by others for molecular data (again mostly
from Thacker, 2009). Our main concern for this paper was the relationships
among blind and cave dwelling forms. For further discussion of goby
relationships see the recently published Biology of Gobies (Patzner et al.,
2011; or papers like Hoese and Gill, 1993; Larson, 2009; or Thacker, 2009).
Besides the five species of Milyeringa
and Typhleotris we also included
blind members of Glossogobius (also
collected in the 2008 trip) and Typhlogobius
in our phylogeny. Less than 1% of described fish species are blind, and a stygobitic
(aquatic cave dwelling) lifestyle has only evolved in 20 families of the 500 or
so families of bony fishes. Stygobitic forms are especially poorly known among
gobies. Besides those mentioned above there is Caecogobius (from Philippine caves), Oxyeleotris (from Papua, and the only blind eleotrid we don’t have
samples for) and a few species of Luciogobius
and Typhlogobius, found in seaside
caves in marine or brackish water). Given the limited number of blind gobies
species known it probably isn’t a surprise that our optimization recovered the
common ancestor of Milyeringa and Typhleotris also as a blind taxon, with independent
origins of blindness recovered for both Glossogobius
and Typhlogobius (Fig 3). When
collecting Glossogobius in Madagascar,
I couldn’t help but notice how different they were from the Typhleotris we collected in the first
part of the trip. We could easily scoop up most individuals of Typhleotris with a simple swipe of a
dipnet (or even our hands) while individuals of Glossogobius ankaranensis were much more skittish and swam away at
almost the same speed as the sighted G.
callidus that we collected in the same caves. Individuals of G. ankaranensis
that we collected were depigmented and blind but you could still see the remnants
of a dark bead-sized lens right where the full eyes would be, implying a more recent
loss of sight. The Typhleotris
species had bone covering the region of the orbit and no eye to speak of. The specimens
of Milyeringa I sampled in Australia
look very much like their cousins in Madagascar. I couldn’t help but note the
red dirt and baobab trees that are also common to the regions where these
fishes are found; I like to image that this must have been what parts of
Gondwana looked like.
Using what
limited data there is on goby fossils, and using a number of outgroups that did
have a good fossil record, we were able to date the divergences across the tree
and as it is related to our node of interest. Incorporating the error bars
around the divergence estimates, we recovered ages that were congruent with the
break up of eastern Gondwana. A couple of caveats come with this: (1) our
phylogeny uses four mitochondrial genes, so it is essentially dated on a single
locus, and, (2) Australia and Madagascar were never directly abutting in any
current Gondwanan model, India and Antarctica were always in between.
Part of the
early criticism we have received for our paper is that we don’t discuss the
basal relationships of the other gobies in our dated phylogeny (see FB thread
below). We didn’t discuss the other non-blind taxa much because we are fully
cognizant of the fact that outside of the subterranean taxa of interest we did
not collect most of the other gobies in our tree. Although certainly our dated
phylogeny is unique, we do think a discussion of gobiiform relationships is
better suited for a paper by those with vested interests in those
relationships. Our interests centered around the relationships among the blind
members. Our tree was the first to incorporate several of these lineages but we
didn’t add many new taxa and no new genes from previous work on Gobiiformes.
Our approach of using Bayesian inference to estimate the phylogeny and
divergence times simultaneously while using a more expansive outgroup sampling
may be novel, but the real work on gobies will have to come from the addition
of morphological and nuclear characters by folks who know these taxa better
than us (I’m looking at you Chris Thacker, Luke Tornabene and others). My
co-authors and I were trying to get a better understanding of the relationships
of the subterranean lineages, so forgive us if we did not mention the rest of
the tree much, or cite particular papers discussing those relationships.
As for caveat #2: are we suggesting
that there are likely cavefishes in India that may be related to Milyeringa and Typhleotris? Or that they were on Antarctica? Possibly, one can
only speculate about “missing” lineages. We continue to discover that our
knowledge of major geological events are not quite as stable as we once
thought. (Remember when the Closure of the Isthmus of Panama was only 3.5mya?)
I think assuming that the current timing and scenario of the break-up of
Gondwana is the last word on the subject would be a mistake. One intriguing
possibility is of a possible direct connection between Madagascar and Australia
in a land connection called Pandora (Parenti and Ebach, 2010). The cavefishes
in their current incarnation as Milyeringa
and Typhletoris are probably not
capable of dispersing much beyond their isolated aquatic cave systems but that
doesn’t mean that the cave systems themselves haven’t moved around and evolved.
More than likely they did, just look at the karst window that gave rise to the
Death Goby. The scenario I picture in my head is of a widespread lineage
probably composed of both cave dwelling and non-subterranean species on eastern
Gondwana; the drifting continents then separated this lineage. Most of the
members of this lineage slowly went extinct with time (while adding a few new
ones now and again) and all that remains today are a handful of species in
isolated caves in Madagascar and Australia. What better way to escape extinction
that to hide out in a cave? (Just ask Al Qaeda.) Of course there are other
potential scenarios, as we discuss in our paper, this one is just the most
palatable for me. However, without evidence of sighted members of the Milyeringa + Typhleotris clade, the simplest conclusion is that the ancestor was
a blind cavefish too (as we report in the paper).
Any way you slice it, the best
explanation we currently have for this lineage of cave dwellers remains that
they are a Gondwanan relict. Given their very limited dispersal ability (blind,
restricted to their cave habitats) and the ancient age we recover for them, it
would seem that this group might be one of the best cases for a group that
shows a vicariant Gondwanan pattern.
References
Chakrabarty, P., (2010) Status and phylogeny of Milyeringidae, with the description of a new blind cave fish from Australia, Milyeringa brooksi, n. sp. Zootaxa 2557:19-28. Chakrabarty, P., Davis, M.P., Sparks, J.S. (2012) First reported case of a trans-oceanic sister-group relationship between vertebrate troglobites. PLoS One 7:e44083 (pg.1-8).
Hoese, D.F. and Gill, A.C. (1993) Phylogenetic relationships of eleotridae fishes (Perciformes: Gobioidei) Bulletin of Marine Science 52: 415-440.
Larson, H.K. (2009) Review of the gobiid fish genera, Eugnathogobius and Pseudogobiopsis (Gobioidei: Gobiidae: Gobionellinae), with descriptions of three new species. The Raffles Bulletin of Zoology 57: 127-181.
Parenti, L.R. and Ebach, M.C. (2010) Wallacea deconstructed. In: Beyond Cladistics: The Branching of a Paradigm (D.M. Williams and S. Knapp, eds.) University of California, pp. 303-318.
Stiassny, M.L.J., Chakrabarty, P. , Loiselle, P. (2001) Relationships of the Madagascan cichlid genus Paretroplus, with a description of a new species from the Betsiboka River drainage of northwestern Madagascar. Ichthyological Explorations of Freshwaters 12: 29 – 40.
Thacker C.E. (2009) Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia 2009: 93–104.