Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

How many species of living sharks, skates and rays are there, and how did theyarise over the course of evolution?
Gavin Naylor1,2 and Neil Aschliman21) Department of Scientific Computing and 2) Department of Biology
Florida State University,Tallahassee, Fl 32306, USA
Contact e-mail: gjpnaylor@gmail.com

Abstract
There are more than 27,000 described species of bony fishes but only about 1,100 named elasmobranchs(including 420+ sharks and 650+ skates and rays). Several hypotheses have been forwarded to explain why
there are so many more kinds of bony fishes than elasmobranchs. Some of the more plausible hypotheses
are based on the fact that teleostean ray-finned fishes experienced whole genome duplication early in theirevolution. It is argued that these whole genome duplications provided the necessary raw material for
evolutionary experimentation and biodiversification in bony fishes, whereas no such opportunity presented
itself for elasmobranchs. However, recent work based on DNA sequence comparisons is uncovering newsharks and rays that were previously not thought to be distinct species. Thus at least some of the apparent
lack of diversity in elasmobranchs may be a consequence of our inability to recognize physically similar but in fact different - species, due to the morphologically conservative evolution of the group. In the current
work we present a DNA sequence survey across elasmobranchs. We show three distinct applications for
DNA sequence comparisons. First, we show that relatively fast-evolving mitochondrial gene sequences canbe useful for verifying species identities in the field. Second, we show that these same sequences can reveal
geographic sub-structure and evolutionary diversity that has previously gone undetected. Finally, we show
how carefully selected gene sequences can be paired with carefully tailored analyses to estimate theevolutionary relationships among distantly related groups of elasmobranchs. This last application can beparticularly challenging, as different genes frequently suggest different evolutionary relationships
depending on the method of analysis used.

Introduction
Humans have long been fascinated by sharks and rays. The fascination, fueled by a mixture of curiosity andfear, probably stems from the fact that these ancient animals live in an environment in which humans arepoorly adapted and in which they are occasionally attacked. Because few people experience directinteractions with these animals, the accounts of those that do tend to be cherished, recycled, embellishedand exaggerated. The number of popular books and film documentaries that repackage old information
about sharks with a new “spin” attests to a seemingly insatiable human interest in these animals.
With the cultural shift toward environmentalism, public opinion about sharks has been changing. PopularNaylor & Aschliman: Evolution of sharks, skates and rays

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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

culture now emphasizes that these animals are not a marine menace, but are instead stewards of theenvironment that play a critical role at the apex of marine food chains. The public is told in plaintive tones
that sharks are misunderstood and that there is a need to study them because fisheries are depleting theirnumbers to such an extent that there will likely be dire consequences for marine ecosystems. As a result, awave of instant “shark researchers” has sprung up all over the world. Most seem to be associated with
tourist diving operations using protective cages. These businesses often cater to a sense of adventure while
offering clients the impression that they are contributing to a scientific understanding of these animals.
Unfortunately, despite considerable press coverage and shifting public awareness, this has done little topromote much needed basic research on chondrichthyan diversity and evolution. In spite of the fact thatmuch of the general public is fascinated with “Shark Week,” we actually know surprisingly little about thebasic biology of these animals. We don’t know how many extant species exist (current estimates suggest
between 1200-1500 [Compagno et al., 2005; P.R. Last, pers. comm.]) .We don’t know the geographic
ranges of most of the described species. We know little about their life histories and almost nothing of theirevolutionary inter-relationships.

Background
Sharks and rays collectively comprise Elasmobranchii or “plate-gilled” fishes. Together with their archaic
relatives the chimaeras, they constitute the Chondrichthyes, or cartilaginous fishes. While chondrichthyans,in the broad sense, have a fossil record that extends back at least 400 million years to the early Devonian,modern sharks and rays did not arise until much later in the Late Triassic or Early Jurassic, about 200
million years ago (Maisey, 1984; Maisey et al., 2004). Today there are about 1,100 named species of living
sharks and rays (Compagno et al., 2005). By contrast there are 27,000 described species of living bony
fishes (Nelson, 2006). Why there are so many more species of bony fishes than elasmobranchs is not
immediately clear, but several hypotheses have been forwarded to explain the differences. These range
from the intrinsic differences in size (the average elasmobranch is generally much larger than the averagebony fish) to differences in fecundity (sharks generally have fewer offspring than do bony fishes) anddifferences in generation time (sharks have much longer generation times than most bony fishes). Morerecently scientists have been drawn toward explanations that are based on genetic architecture.
Comparative genomic studies indicate that bony fishes have had at least one complete genome duplicationthat was not shared by their chondrichthyan counterparts. The argument is made that the extra genetic
material provided by this whole genome duplication may have provided more raw material for evolutionary
experimentation in bony fishes than in chondrichthyans (reviewed by Donoghue & Purnell, 2005).
While a genome duplication would “free up” components of an organism’s genetic architecture to explore
new configurations, the associated constraint release would also foster faster rates of evolution in thecomponent parts of the architecture. Such speed-ups would cause bony fishes to diverge away from theirancestral condition at a faster rate than chondrichthyans. This has important implications for comparative
vertebrate biology. If we are interested in identifying the attributes that made vertebrates so successful, it isNaylor & Aschliman: Evolution of sharks, skates and rays

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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

important to identify the ancestral vertebrate condition. This is much more easily done when there has been
little evolutionary change from the starting point. Because elasmobranchs have not undergone theaccelerated rates of evolution that are seen in the bony fishes, they are likely much closer to those of theancestral vertebrate condition. Indeed recent work by Venkatesh’s group has shown that the elephant shark
genome is architecturally more similar to that of mammals than is the genome of bony fishes, even thoughbony fishes are more closely related to mammals (Venkatesh et al., 2007). It is likely that chondrichthyans
will play an increasingly important role in comparative genomic studies in the near future.

Diversity within elasmobranchs and the use of sequence comparisonsElasmobranchs are not merely ciphers to shed light on vertebrate origins. They have attributes that makethem useful for understanding multiple aspects of the evolutionary process. Because they are a relatively
old group, we can use them as to explore the effects of plate tectonics on the distribution of marineorganisms (e.g. Long, 1994); because they have a relatively dense fossil record we can use them to measurerates of molecular and morphological evolution; and because they exhibit such tremendous variation in life
history traits we can use them to explore life history trait evolution (e.g. Musick & Ellis, 2005).
Somewhat surprisingly, there has been relatively little interest in understanding relationships withinelasmobranchs, until Drs. Nakaya and Compagno brought attention to their diversity in the 1970’s(Compagno 1973, 1977). In our own work, inspired by the work of Drs. Nakaya and Compagno, we haveset out to explore the diversity and evolutionary relationships among the lineages of elasmobranchs guidedby patterns seen in DNA sequence data. Over the past 25 years, we have amassed more than 5000 tissue
samples from approximately 400 different species of elasmobranchs. We have employed DNA sequences
as markers in multiple contexts. At a very basic and practical level we have used the fast evolving
mitochondrial sequence ND2 to validate our field identifications, something that is especially importantwhen dealing with morphologically conservative groups such as elasmobranchs. Second, we have used thevery same ND2 sequences as markers to shed light on population substructure within species. Third, wehave used a combination of single copy genes from both the nuclear (RAG1) and mitochondrial(cytochrome B, ND2 and ND4) genomes to estimate the phylogenetic relationships among the majorgroups of extant elasmobranchs. Our phylogenetic work has focused on representation at the generic level.
We have taken steps to ensure a balanced sampling of taxa to represent all of the major morphologicalgroups. Finally, because the current symposium is focused on understanding reproduction in aquaticanimals, we have taken this opportunity to use the phylogenetic tree estimated from both nuclear andmitochondrial markers to shed light on the evolution of different modes of reproduction in elasmobranchs.
In what follows, we present empirical examples employing sequence comparisons in the three levels ofanalysis to give a sense of the breadth of application and utility of comparative sequence data.

Field ID validation
In a recent survey of the elamobranch diversity, we sequenced every animal in our tissue database for theNaylor & Aschliman: Evolution of sharks, skates and rays

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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

fast-evolving mitochondrial gene ND2. The sequences were aligned and subjected to Neighbor Joining
analysis. In several instances, we quickly discovered that animals identified as one species in the field weregenetically identical to specimens that were originally identified as different species. In Figure 1 we present
one such example in which an animal identified as Dasyatis was actually a specimen of Himantura gerrardi.
In some scientific circles, it is common practice to base assessments from a single individual to represent aspecies. If a mistake is made in identifying the species, then the reported results may be invalid. Inaccurate
species identification likely impacts many online databases such as GenBank, because there are no species
validation requirements that must be met before submitting sequencing information. People using these
databases should therefore be cautious about drawing strong conclusions unless they have independent
means of validating their claims.

Figure 1.

Example showing how neighbor-joining

analysis of aligned ND2 sequences reveals that a specimen(mis) identified in the field as Dasyatis sp. is actually a
specimen of Himatura gerardi.

Geographic structure of populations
When subjecting mitochondrial DNA sequence data to Neighbor Joining analysis we observed several
instances in which distinct geographic substructure is evident within species. In some instances thedivergence between populations is larger than the divergence seen between recognized, distinct species,
suggesting that revision to the current taxonomy may be warranted.
For the purposes of this contribution we bring attention to geographic substructuring seen in three different
species of sharks: the black tip shark Carcharhinus limbatus, the Sand-bar shark Carcharhinus plumbeus,
and the silky shark Carcharhinus falciformis. In all three cases there is a clear distinction between
populations from the Indo-West Pacific and from the North Atlantic (Figure 2). It is intriguing that in thecase of C. limbatus, the Indo-West Pacific population appears more closely related to a different species(the graceful shark Carcharhinus amblyrhnchoides) than it does to the North Atlantic population of C.
limbatus. Similarly, the Indo-West Pacific population of C. plumbeus appears more similar to the big-nose
shark (Carcharhinus altimus) than it does to North Atlantic C. plumbeus. This may indicate that theIndo-West Pacific populations of both C. plumbeus and C. limbatus are different species from their North
Atlantic counterparts. However, this needs to be confirmed with independent nuclear markers as it is also
possible that it is a reflection of lineage sorting of ancestral haplotypes.
Naylor & Aschliman: Evolution of sharks, skates and rays8Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

Figure 2. Neighbor-joining trees depicting within-species relationships for three different species (C. falciformis, C.
limbatus and C plumbeus). In all three cases there is a clear distinction between North Atlantic and Indo-Pacificpopulations. In the case of C. limbatus it appears that the Indo-Pacific population of C. limbatus is more closely related
to the graceful shark C. amblyrhynchoides than it is to the North Atlantic population of C. limbatus. In a similar vein
the Western Atlantic population of C. plumbeus appears closer to the Big-nose shark C. altimus than it does to theIndo-Pacific population of C. plumbeus.

Phylogeny
While clustering fast-evolving mitochondrial sequences with Neighbor Joining can be useful for assessing
sequence similarity among closely related organisms, the efficacy of the approach diminishes forcomparisons among more distant taxa. This is partly because multiple hits in fast evolving sequences erase
phylogenetic signal, and partly because of shortcomings intrinsic to applying distance-based approaches tophylogenetic estmation. In order to estimate phylogeny, we need to collect data with rates of change better
suited to estimating deeper divergences. Furthermore, steps must be taken to ensure that the comparisons
made are among orthologous rather than paralogous copies of the target marker gene. In general this isdone by amplifying a gene that is only present in a single copy among the organisms being compared.
Finally, when attempting to estimate phylogenetic relationships among distantly related taxa, it is importantthat the sampling of taxa across the evolutionary process be as even as possible.
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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

For the tree that we present in this symposium (Figure 3), we used the mitochondrial genes ND2, cytB andND4, and the single-copy nuclear gene RAG1. Our analyses were carried out at the amino acid level (asopposed to the nucleotide level) using a mixture model in a Bayesian framework (MRBAYES: Ronquist &Huelsenbeck, 2003).

Figure 3. Estimated tree of relationships among the major groups of elasmobranchs based on Bayesian analysis of
mitochondrial and nuclear protein coding sequence data.

Using phylogenies to understand trait evolution and make predictions.
We have used the phylogeny shown in figure 3 as a framework on which to map the distribution ofreproductive traits in elasmobranchs. We assigned states for one of five modes of reproduction to eachtaxon, based on the coding scheme of Dulvy and Reynolds (1997). The categories were (1) oviparity; (2)yolk sac ovoviviparity; (3) ovoviviparity with maternal input through histotroph; (4) oophagy/cannibalism;(5) placental viviparity.
When plotted onto the tree it is possible to deduce the number of times different strategies arose over thecourse of evolution. Several things are striking from the distribution shown in Figure 4. However herein wefocus on two that are especially revealing. The first is that there are both ovoviviparous and species withplacental viviparity within the genus Mustelus. This suggests that changing strategies over the course ofNaylor & Aschliman: Evolution of sharks, skates and rays

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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproduction

evolution is not especially difficult, which can also be deduced from the fact that there have clearly been
numerous changes in strategy over the entire tree. The second observation is controversial. Pristis is thesole member of a clade of organisms that is reported in the literature to exhibit yolk sac only ovoviparity.
Except for the oviparous skates, all of its immediate relatives (the rays) employ maternal nutrition in theform of histotroph to nourish their young. This can be in the form of lipid-rich histotroph exhibited bystingrays, or limited histotrophy suspected in most other batoid fishes. The embryos of some species of
Pristis are born at greater than a meter in length. It would seem highly unlikely that an animal of this size
could be supported by yolk reserves alone. We conjecture that this is an error in the literature and thatpristids, like the closely related rays, employ a form of maternal supplementing of the yolk sac reserves.
This is a prediction based on the phylogenetic position of Pristis in the tree, but one that needs to bechecked empirically.

Figure 4. Different modes of reproduction, taken from Dulvy and Reynolds (1997) plotted on to the phylogenetic treeof relationships seen in Fig. 3.

Conclusions
While there is considerable diversity within modern elasmobranchs, much of it remains poorly known. We
are attempting to characterize extant

diversity using molecular techniques and hope to provide a rigorous

evolutionary framework that subsequent researchers can use to explore character evolution within theNaylor & Aschliman: Evolution of sharks, skates and rays

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Reproduction of Marine Life, Birth of New Life! Investigating the Mysteries of Reproductiongroup. We hope that our documenting the extant diversity in the group will catalyze much needed further
exploration .

References
Compagno, L. J. V. 1973. Interrelationships of living elasmobranchs. In P. H. Greenwood, R. S. Miles andC. Patterson, eds, Interrelationships of Fishes. Academic Press, pp. 15-61.
Compagno, L. J. V. 1977. Phyletic relationships of living sharks and rays. American Zoologist 17(2):303-322.
Compagno, L. J. V., D. A. Didier and G. H. Burgess. 2005. Classification of chondrichthyan fish. In Fowler,S. L., R. D. Cavanagh, M. Camhi, G. H. Burgess, G. M. Caillet, S. V. Fordham, C. A. Simpfendorfer andJ. A. Musick, comp. and eds, Sharks, Rays, and Chimaeras: The Status of the Chondrichthyan Fishes.
Status Survey. IUCN, Gland, Switzerland and Cambridge, UK, pp. 4-11.
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Musick, J. A. and J. K. Ellis. 2005. Reproductive evolution of Chondrichthyans. In Hamlett, W. C., ed.,Reproductive Biology and Phylogeny of Chondrichthyes: Sharks, batoids and chimaeras. Science
Publishers, Enfield, NH. pp 45-79.
Nelson, J. S. 2006. Fishes of the world. Fourth ed. John Wiley and Sons, Inc., New York, NY.
Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference undermixed models. Bioinformatics 19:1572-1574.
Venkatesh, B., E. F. Kirkness, Y. Loh, A. L. Halpern, A. P. Lee, J. Johnson, N. Dandona, L. D. Viswanathan,A. Tay, J. C. Venter, R. L. Strausberg, S. Brenner. 2007. Survey sequencing anｄcomparative analysis of
the elephant shark (Callorhynchus milii) genome. PLoS Biology 5(4): 932-944.

Author’s current address
1) G. Naylor: Hollings Marine Lab, 331 Fort Johnson Rd, Charleston, SC 29412, USA2) N. Aschliman: Biology Department Lewis Hall 202A, 518 W. Locust Street, Davenport, Iowa 52803, USA

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