Scientists find missing link between whale and its closest relative, the hippo

A group of four-footed mammals that flourished worldwide for 40 million years and then died out in the ice ages is the missing link between the whale and its not-so-obvious nearest relative, the hippopotamus.

The conclusion by University of California, Berkeley, post-doctoral fellow Jean-Renaud Boisserie and his French colleagues finally puts to rest the long-standing notion that the hippo is actually related to the pig or to its close relative, the South American peccary. In doing so, the finding reconciles the fossil record with the 20-year-old claim that molecular evidence points to the whale as the closest relative of the hippo.

"The problem with hippos is, if you look at the general shape of the animal it could be related to horses, as the ancient Greeks thought, or pigs, as modern scientists thought, while molecular phylogeny shows a close relationship with whales," said Boisserie. "But cetaceans – whales, porpoises and dolphins – don't look anything like hippos. There is a 40-million-year gap between fossils of early cetaceans and early hippos."

In a paper appearing this week in the Online Early Edition of the Proceedings of the National Academy of Sciences, Boisserie and colleagues Michel Brunet and Fabrice Lihoreau fill in this gap by proposing that whales and hippos had a common water-loving ancestor 50 to 60 million years ago that evolved and split into two groups: the early cetaceans, which eventually spurned land altogether and became totally aquatic; and a large and diverse group of four-legged beasts called anthracotheres. The pig-like anthracotheres, which blossomed over a 40-million-year period into at least 37 distinct genera on all continents except Oceania and South America, died out less than 2 and a half million years ago, leaving only one descendent: the hippopotamus.

This proposal places whales squarely within the large group of cloven-hoofed mammals (even-toed ungulates) known collectively as the Artiodactyla – the group that includes cows, pigs, sheep, antelopes, camels, giraffes and most of the large land animals. Rather than separating whales from the rest of the mammals, the new study supports a 1997 proposal to place the legless whales and dolphins together with the cloven-hoofed mammals in a group named Cetartiodactyla.

"Our study shows that these groups are not as unrelated as thought by morphologists," Boisserie said, referring to scientists who classify organisms based on their physical characteristics or morphology. "Cetaceans are artiodactyls, but very derived artiodactyls."

The origin of hippos has been debated vociferously for nearly 200 years, ever since the animals were rediscovered by pioneering French paleontologist Georges Cuvier and others. Their conclusion that hippos are closely related to pigs and peccaries was based primarily on their interpretation of the ridges on the molars of these species, Boisserie said.

"In this particular case, you can't really rely on the dentition, however," Boisserie said. "Teeth are the best preserved and most numerous fossils, and analysis of teeth is very important in paleontology, but they are subject to lots of environmental processes and can quickly adapt to the outside world. So, most characteristics are not dependable indications of relationships between major groups of mammals. Teeth are not as reliable as people thought."

As scientists found more fossils of early hippos and anthracotheres, a competing hypothesis roiled the waters: that hippos are descendents of the anthracotheres.

All this was thrown into disarray in 1985 when UC Berkeley's Vincent Sarich, a pioneer of the field of molecular evolution and now a professor emeritus of anthropology, analyzed blood proteins and saw a close relationship between hippos and whales. A subsequent analysis of mitochondrial, nuclear and ribosomal DNA only solidified this relationship.

Though most biologists now agree that whales and hippos are first cousins, they continue to clash over how whales and hippos are related, and where they belong within the even-toed ungulates, the artiodactyls. A major roadblock to linking whales with hippos was the lack of any fossils that appeared intermediate between the two. In fact, it was a bit embarrassing for paleontologists because the claimed link between the two would mean that one of the major radiations of mammals – the one that led to cetaceans, which represent the most successful re-adaptation to life in water – had an origin deeply nested within the artiodactyls, and that morphologists had failed to recognize it.

This new analysis finally brings the fossil evidence into accord with the molecular data, showing that whales and hippos indeed are one another's closest relatives.

"This work provides another important step for the reconciliation between molecular- and morphology-based phylogenies, and indicates new tracks for research on emergence of cetaceans," Boisserie said.

Boisserie became a hippo specialist while digging with Brunet for early human ancestors in the African republic of Chad. Most hominid fossils earlier than about 2 million years ago are found in association with hippo fossils, implying that they lived in the same biotopes and that hippos later became a source of food for our distant ancestors. Hippos first developed in Africa 16 million years ago and exploded in number around 8 million years ago, Boisserie said.

Now a post-doctoral fellow in the Human Evolution Research Center run by integrative biology professor Tim White at UC Berkeley, Boisserie decided to attempt a resolution of the conflict between the molecular data and the fossil record. New whale fossils discovered in Pakistan in 2001, some of which have limb characteristics similar to artiodactyls, drew a more certain link between whales and artiodactyls. Boisserie and his colleagues conducted a phylogenetic analysis of new and previous hippo, whale and anthracothere fossils and were able to argue persuasively that anthracotheres are the missing link between hippos and cetaceans.

While the common ancestor of cetaceans and anthracotheres probably wasn't fully aquatic, it likely lived around water, he said. And while many anthracotheres appear to have been adapted to life in water, all of the youngest fossils of anthracotheres, hippos and cetaceans are aquatic or semi-aquatic.

"Our study is the most complete to date, including lots of different taxa and a lot of new characteristics," Boisserie said. "Our results are very robust and a good alternative to our findings is still to be formulated."

Brunet is associated with the Laboratoire de Géobiologie, Biochronologie et Paléontologie Humaine at the Université de Poitiers and with the Collège de France in Paris. Lihoreau is a post-doctoral fellow in the Département de Paléontologie of the Université de N'Djaména in Chad.

The work was supported in part by the Mission Paléoanthropologique Franco-Tchadienne, which is co-directed by Brunet and Patrick Vignaud of the Université de Poitiers, and in part by funds to Boisserie from the Fondation Fyssen, the French Ministère des Affaires Etrangères and the National Science Foundation's Revealing Hominid Origins Initiative, which is co-directed by Tim White and Clark Howell of UC Berkeley.

Bacterial flagella and eukaryotic cilia are irreducibly complex, Since nonfunctional intermediates cannot be preserved by natural selection, these systems can only be explained by intelligent design.
Source:
Behe, Michael J., 1996. Darwin's Black Box, New York: The Free Press, pp. 59-73.
Response:
This is an example of argument from incredulity, because irreducible complexity can evolve naturally. Many of the proteins in the bacterial flagellum or eukaryotic cilium are similar to each other or to proteins for other functions. Their origins can easily be explained by a series of gene duplication events followed by modification and/or cooption, proceeding gradually through intermediate systems different from and simpler than the final flagellum.

One plausible path for the evolution of flagella goes through the following basic stages (keep in mind that this is a summary, and that each major cooption event would be followed by long periods of gradual optimization of function):

A passive, nonspecific pore evolved into a more specific passive pore by addition of gating protein(s). Passive transport was converted to active transport by addition of an ATPase that coupled ATP hydrolysis to improved export capability. This complex formed a primitive type III export system.

The type III export system is converted to a type III secretion system (T3SS) by addition of outer membrane pore proteins (secretin and secretin chaperone) from the type II secretion system. These eventually form the P- and L-rings, respectively, of modern flagella. The modern type III secretory system forms a structure strikingly similar to the rod and ring structure of the flagellum [Hueck 1998; Blocker et al. 2003].

The T3SS secreted several proteins, one of which was an adhesin (a protein that sticks the cell to other cells or to a substrate). Polymerization of this adhesin forms a primitive pilus, an extension which gives the cell improved adhesive capability. After the evolution of the T3SS pilus, the pilus diversifies for various more specialized tasks by duplication and subfunctionalization of the pilus proteins (pilins).

An ion pump complex with another function in the cell fortuitously becomes associated with the base of the secretion system structure, converting the pilus into a primitive proto-flagellum. The initial function of the protoflagellum is improved dispersal. Homologs of the motor proteins, MotA and MotB, are known to function in diverse prokaryotes independently of the flagellum.

The binding of a signal transduction protein to the base of the secretion system regulates the speed of rotation depending on the metabolic health of the cell. This imposes a drift towards favorable regions and away from nutrient-poor regions, such as those found in overcrowded habitats. This is the beginning of chemotactic motility.

Numerous improvements follow the origin of the crudely functioning flagellum. Notably, many of the different axial proteins (rod, hook, linkers, filament, caps) originate by duplication and subfunctionalization of pilins or the primitive flagellar axial structure. These proteins end up forming the axial protein family.

The eukaryotic cilium (also called the eukaryotic flagellum or undulipodium) is fundamentally different from the bacterial flagellum. It probably originated as an outgrowth of the mitotic spindle in a primitive eukaryote (both structures make use of sliding microtubules and dyneins). Cavalier-Smith [1987; 2002] has discussed the origin of these systems on several occasions.

The bacterial flagellum is not even irreducible. Some bacterial flagella function without the L- and P-rings. In experiments with various bacteria, some components (e.g. FliH, FliD (cap), and the muramidase domain of FlgJ) have been found helpful but not absolutely essential [Matzke 2003]. One third of the 497 amino acids of flagellin have been cut out without harming its function [Kuwajima 1988]. Furthermore, many bacteria have additional proteins that are required for their own flagella but which are not required in the "standard," well-studied flagellum found in E. coli. Different bacteria have different numbers of flagellar proteins (in Helicobacter pylori, for example, only 33 proteins are necessary to produce a working flagellum), so Behe's favorite example of irreducibility seems actually to exhibit quite a bit of variability in terms of numbers of required parts [Ussery 1999].

Eukaryotic cilia are made by more than 200 distinct proteins, but even here irreducibility is illusive. Behe (1996) implied, and Denton (1986, 108) claimed explicitly, that the common "9+2" tubulin structure of cilia could not be substantially simplified. Yet functional 3+0 cilia, lacking many microtubules as well as some of the dynein linkers, are known to exist [Miller 2003, 2004].

Eubacterial flagella, archebacterial flagella, and cilia use entirely different designs for the same function. That is to be expected if they evolved separately, but it makes no sense if they were the work of the same designer.
Links:
Matzke, N. J., 2003. Evolution in (brownian) space: a model for the origin of the bacterial flagellum. http://www.talkdesign.org/faqs/flagellum.html or http://www.talkreason.org/articles/flag.pdf (see also 'Background to "Evolution in (Brownian) space"', http://www.talkdesign.org/faqs/flagellum_background.html or http://www.talkreason.org/articles/flagback.cfm)

Dunkelberg, Pete, 2003. Irreducible complexity demystified http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html

Musgrave, Ian, 2000. Evolution of the bacterial flagella. http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella.htm
References:
Blocker, Ariel, Kaoru Komoriya, and Shin-Ichi Aizawa, 2003. Type III secretion systems and bacterial flagella: Insights into their function from structural similarities. Proceedings of the National Academy of Science USA 100(6): 3027-3030. http://www.pnas.org/cgi/content/full/100/6/3027
Cavalier-Smith, T., 1987. The origin of eukaryote and archaebacterial cells. Annals of the New York Academy of Sciences 503: 17-54.
Cavalier-Smith, T., 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52: 297-354.
Denton, M., 1986. Evolution: A Theory in Crisis. Bethesda, MD: Adler & Adler.
Hueck, C. J., 1998. Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiology and Molecular Biology Reviews 62: 379-433.
Kuwajima, G., 1988. Construction of a minimum-size functional flagellin of Escherichia coli. Journal of Bacteriology 170: 3305-3309.
Matzke, N. J., 2003. (see above)
Miller, K., 2003. Answering the biochemical argument from design. in: Manson, N. (Ed.), God and design: the teleological argument and modern science, Routledge, London, pp. 292-307. http://www.millerandlevine.com/km/evol/design1/article.html
Miller, K., 2004. The Flagellum Unspun, in: Dembski, W., and Ruse, M. (Eds.), Debating Design: from Darwin to DNA, Cambridge University Press, New York. http://www.millerandlevine.com/km/evol/design2/article.html
Ussery, D., 1999. (see below)
Further Reading:
Ussery, David, 1999. A biochemist's response to "The biochemical challenge to evolution". Bios 70: 40-45. http://www.cbs.dtu.dk/staff/dave/Behe.html

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